University of Washington - SAFS - Roberts Lab

This notebook is part of the coral E5 timeseries_molecular project (GitHub repo). Due to the desire to have some preliminary data to use for a presentation, Steven wanted…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Bismark Alignments - A.pulchra Trimmed Reads Using Bismark on Hyak

2025

Bismark

Acropora pulchra

coral

timeseries_molecular

klone

hyak

alignment

WGBS

In preparation for a quick Bismark alignment, per Steven’s request (GitHub Issue), I needed to generate a bisulfite-converted genome for A.pulchra, as one did not already…

<<<<<<< HEAD

This notebook is part of the coral E5 timeseries_molecular project (GitHub repo). Whole genome bisulfite sequencing (WGBS) data was received on 20241230 (Notebook entry) and…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Trimming - A.pulchra WGBS with fastp FastQC and MultiQC on Raven

2025

Acopora pulchra

WGBS

<<<<<<< HEAD

=======

trimming

fastp

FastQC

MultiQC

Raven

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

This notebook is part of the coral E5 timeseries_molecular project (GitHub repo). Whole genome bisulfite sequencing (WGBS) data was received on 20241230 (Notebook entry) and…

<<<<<<< HEAD

In preparation for a quick Bismark alignment, per Steven’s request (GitHub Issue), I needed to generate a bisulfite-converted genome for A.pulchra, as one did not already…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Bisulfite Genome - A.pulchra BS Genome Using Bismark

2025

Acropora pulchra

bismark

bisulfite

coral

timeseries_molecular

The notebook entry is part of the coral E5 molecular_timeseries project (GitHub repo). I ran FastQC and MultiQC on the A.pulchra WGBS data received on 20241230 in…

FastQC MultiQC - A.pulchra WGBS E5 Timeseries

2024

timeseries_molecular

WGBS

Acropora pulchra

FastQC

MultiQC

Dec 31, 2024

The notebook entry is part of the coral E5 molecular_timeseries project (GitHub repo). I ran FastQC and MultiQC on the A.pulchra WGBS data received on 20241230 in…

<<<<<<< HEAD

Dec 31, 2024

We received whole genome bisulfite sequencing (WGBS) data from Azenta project 30-1067895835. All files were downloaded and MD5 checksums were verified. Raw FastQ files are…

Data Received - S.pacificus WGBS Data from Azenta Project 30-1067895835

2024

WGBS

BS-seq

Data Received

bisulfite

30-1067895835

Somniosus pacificus

sleeper shark

We received whole genome bisulfite sequencing (WGBS) data from Azenta project 30-1067895835 as part of the urol-e5/timeseries_molecular project (GitHub repo). All files were…

Data Received - Coral E5 WGBS Time Series from Azenta Project 30-1067895835

2024

30-1067895835

WGBS

BS-seq

bisulfite

Data Received

timeseries_molecular

We received whole genome bisulfite sequencing (WGBS) data from Azenta project 30-1067895835 as part of the urol-e5/timeseries_molecular project (GitHub repo). All files were…

<<<<<<< HEAD

We received whole genome bisulfite sequencing (WGBS) data from Azenta project 30-1067895835. All files were downloaded and MD5 checksums were verified. Raw FastQ files are…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Received - S.pacificus WGBS Data from Azenta Project 30-1067895835

2024

WGBS

BS-seq

Data Received

bisulfite

30-1067895835

Somniosus pacificus

sleeper shark

We received whole genome bisulfite sequencing (WGBS) data from Azenta project 30-1067895835. All files were downloaded and MD5 checksums were verified. Raw FastQ files are…

Data Received - G.macrocephalus WGBS Data from Azenta Project 30-1067895835

2024

WGBS

BS-seq

Data Received

bisulfite

30-1067895835

Pacific cod

Gadus macrocephalus

We received whole genome bisulfite sequencing (WGBS) data from Azenta project 30-1067895835. All files were downloaded and MD5 checksums were verified. Raw FastQ files are…

<<<<<<< HEAD

This notebook performs pair-wise comparisons of qPCR gene expression, normalized to GAPDH expression. It calculates delta Cq, delta delta Cq, and fold changes in expression.…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR Analysis - C.gigas Lifestages Carryover

2024

Crassostrea gigas

Pacific oyster

qPCR

project-gigas-carryover

lifestage_carryover

Dec 20, 2024

This notebook performs pair-wise comparisons of qPCR gene expression, normalized to GAPDH expression. It calculates delta Cq, delta delta Cq, and fold changes in expression.…

<<<<<<< HEAD

Dec 20, 2024

Continuing work with project-gigas-carryover lifestage_carryover (GitHub repo) after creating cDNA on 20241024 (Notebook entry), it was finally time to run the qPCRs. Three…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - C.gigas Lifestage Carryover VIPERIN

2024

Crassostrea gigas

Pacific oyster

SsoFast

CFX Connect

CFX96

project-gigas-carryover

VIPERIN

Dec 12, 2024

Continuing work with project-gigas-carryover lifestage_carryover (GitHub repo) after creating cDNA on 20241024 (Notebook entry), it was finally time to run the qPCRs. Three…

<<<<<<< HEAD

Dec 12, 2024

Continuing work with project-gigas-carryover lifestage_carryover (GitHub repo) after creating cDNA on 20241024, it was finally time to run the qPCRs. Three primer sets were…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCRs - C.gigas Lifestage Carryover citrate synthase DNMT1 HSP70 and HSP90

2024

Crassostrea gigas

Pacific oyster

SsoFast

CFX Connect

CFX96

project-gigas-carryover

citrate synthase

DNMT1

HSP70

HSP90

Dec 11, 2024

Continuing work with project-gigas-carryover lifestage_carryover (GitHub repo) after creating cDNA on 20241024, it was finally time to run the qPCRs. Three primer sets were…

<<<<<<< HEAD

Dec 11, 2024

This notebook is part of project-clam-oa (GitHub repo).

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

miRNA Identification - R.phillipinarum sRNA-seq Using ShortStack and miRBase Mature miRNAs

2024

Ruditapes phillipinarum

Manila clam

<<<<<<< HEAD

=======

sRNA-seq

miRNA

project-clam-oa

ShortStack

miRBase

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

This notebook is part of project-clam-oa (GitHub repo).

<<<<<<< HEAD

Continuing work with project-gigas-carryover lifestage_carryover (GitHub repo) after creating cDNA on 20241024, it was finally time to run the qPCRs.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCRs - C.gigas Lifestage Carryover GAPDH ATP_synthase and cGAS

2024

Crassostrea gigas

Pacific oyster

GAPDH

ATP synthase

cGAS

SsoFast

CFX Connect

CFX96

project-gigas-carryover

Continuing work with project-gigas-carryover lifestage_carryover (GitHub repo) after creating cDNA on 20241024, it was finally time to run the qPCRs.

<<<<<<< HEAD

We received sRNA-seq data from Azenta project 30-1069297013. is in. All files were downloaded and MD5 checksums were verified. Raw FastQ files are available here:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Received - Coral E5 sRNA-seq Time Series Azenta Project 30-1069297013

2024

coral

sRNA-seq

timeseries_molecular

Data Received

30-1069297013

This notebook is part of project-clam-oa (GitHub repo).

Trimming and Merging - R.philippinarum sRNA-seq Data Using fastp FastQC and MultiQC

2024

Ruditapes philippinarum

Manila clam

project-clam-oa

sRNA-seq

Dec 6, 2024

This notebook is part of project-clam-oa (GitHub repo).

<<<<<<< HEAD

Dec 6, 2024

This notebook is part of project-clam-oa (GitHub repo).

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

FastQ Concatentation and QC - R.philippinarum sRNA-seq Data Using FastQC and MultiQC

2024

Manila clam

Ruditapes philippinarum

30-1035633055

30-1035633055-TS01

project-clam-oa

FastQC

MultiQC

Dec 5, 2024

This notebook is part of project-clam-oa (GitHub repo).

<<<<<<< HEAD

Dec 5, 2024

This notebook is part of the ceasmallr (GitHub repo) project, comparing DNA methylation in Crassostrea virginica (Eastern oyster) larvae and zygotes, via whole-genome…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Methylation Extraction - C.virginica CEASMALLR WGBS Using Bismark

2024

Crassostrea virginica

Eastern oyster

ceasmallr

wgbs

BS-seq

Bismark

methylation extraction

Nov 26, 2024

This notebook is part of the ceasmallr (GitHub repo) project, comparing DNA methylation in Crassostrea virginica (Eastern oyster) larvae and zygotes, via whole-genome…

<<<<<<< HEAD

Nov 26, 2024

This notebook is part of the ceasmallr (GitHub repo) project, comparing DNA methylation in Crassostrea virginica (Eastern oyster) larvae and zygotes, via whole-genome…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Deduplication - C.virginica CEASMALLR WGBS Using Bismark

2024

Crassostrea virginica

Eastern oyster

ceasmallr

Bismark

WGBS

BS-seq

deduplication

Nov 25, 2024

This notebook is part of the ceasmallr (GitHub repo) project, comparing DNA methylation in Crassostrea virginica (Eastern oyster) larvae and zygotes, via whole-genome…

<<<<<<< HEAD

Nov 25, 2024

Gannet was inaccessible, so went into lab to investigate. When I arrived, Gannet appeared to be powered on and the “Status” light was green, but none of the drive light…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Computer Management - Replace Failed Hard Drive on Gannet

2024

Gannet

HDD

Computer Management

Gannet was inaccessible, so went into lab to investigate. When I arrived, Gannet appeared to be powered on and the “Status” light was green, but none of the drive light…

<<<<<<< HEAD

This notebook is part of the ceasmallr (GitHub repo) project, comparing DNA methylation in Crassostrea virginica (Eastern oyster) larvae and zygotes, via whole-genome…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Alignment - C.virginica CEASMALLR WGBS Using Bismark on Klone Array

2024

trimming

Crassostrea virginica

Eastern oyster

ceasmallr

WGBS

BS-seq

Klone

Bismark

This notebook is part of the ceasmallr (GitHub repo) project, comparing DNA methylation in Crassostrea virginica (Eastern oyster) larvae and zygotes, via whole-genome…

<<<<<<< HEAD

This notebook is part of the ceasmallr (GitHub repo) project, comparing DNA methylation in Crassostrea virginica (Eastern oyster) larvae and zygotes, via whole-genome…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Trimming and QC - C.virginica CEASMALLR FastQs Using fastp BBTools and FastQC-MultiQC

2024

trimming

FastQC

fastp

BBTools

MultiQC

Crassostrea virginica

WGBS

BS-seq

bisulfite

Eastern oyster

ceasmallr

Nov 15, 2024

This notebook is part of the ceasmallr (GitHub repo) project, comparing DNA methylation in Crassostrea virginica (Eastern oyster) larvae and zygotes, via whole-genome…

<<<<<<< HEAD

Nov 15, 2024

In preparation for a grant proposal involving sea star wasting disease, due in about two weeks, Steven asked that I perform taxonomic classification on a Trinity assembly of…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Taxonomic Classification - Trinity Assembly of Unmapped P.helianthoides RNA-seq Using DIAMOND BLASTx and MEGAN6 on Mox

2024

DIAMOND

BLASTx

MEGAN6

Pycnopodia helianthoides

sunflower sea star

Mox

Nov 8, 2024

In preparation for a grant proposal involving sea star wasting disease, due in about two weeks, Steven asked that I perform taxonomic classification on a Trinity assembly of…

<<<<<<< HEAD

Nov 8, 2024

This is part of Chris’ project-mytilus-methylation(GitHub repo). Data was received from Psomagen on 20241101 (Notebook entry). I performed the initial QC using FastQC and Mul…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

FastQ QC - M.trossulus WGBS from Psomagen Using FastQC and MultiQC

2024

Mytilus trossulus

WGBS

Psomagen

FastQC

MultiQC

mussel

project-mytilus-methylation

This is part of Chris’ project-mytilus-methylation(GitHub repo). Data was received from Psomagen on 20241101 (Notebook entry). I performed the initial QC using FastQC and Mul…

<<<<<<< HEAD

This is part of Chris’ project-mytilus-methylation(GitHub repo). Data was received from Psomagen on 20241101 (Notebook entry). I performed the initial QC using FastQC and Mul…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Trimming and QC - M.trossulus WGBS Using fastp and FastQC-MultiQC

2024

Mytilus trossulus

WGBS

fastp

FastQC

MultiQC

bay mussel

project-mytilus-methylation

trimming

This is part of Chris’ project-mytilus-methylation(GitHub repo). Data was received from Psomagen on 20241101 (Notebook entry). I performed the initial QC using FastQC and Mul…

<<<<<<< HEAD

This notebook consists of a markdown rendering of 01-GO-to-GOslim.Rmd (commit: 04a796d).

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Wrangling - GO to GOslims for Graces Dermasterias imbricata Project from Trinity Assembly Genes

2024

Dermasterias imbricata

GOslim

gene ontology

Trinity

Leather star

This notebook consists of a markdown rendering of 01-GO-to-GOslim.Rmd (commit: 04a796d).

<<<<<<< HEAD

This notebook consists of a markdown rendering of 01-GO-to-GOslim.Rmd (commit: 3b642b4).

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Wrangling - GO to GOslims for Graces Pycnopodia helianthoides Project from Trinity Assembly Genes

2024

gene ontology

GOslim

Pycnopodia helianthoides

Trinity

Sunflower sea star

This notebook consists of a markdown rendering of 01-GO-to-GOslim.Rmd (commit: 3b642b4).

<<<<<<< HEAD

In preparation for a grant proposal involving sea star wasting disease, due in about two weeks, Steven asked that I perform taxonomic classification on unmapped…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Sequencing Read Taxonomic Classification - Unmapped P.helanthoides RNA-seq Using DIAMOND-BLASTx and MEGAN6 on Mox

2024

MEGAN6

RNAseq

DIAMOND

BLASTx

Pycnopodia helianthoides

sunflower sea star

Mox

Nov 5, 2024

In preparation for a grant proposal involving sea star wasting disease, due in about two weeks, Steven asked that I perform taxonomic classification on unmapped…

<<<<<<< HEAD

Nov 5, 2024

Received supplemental sRNA-seq data for Azenta Project 30-1035633055, since the previous data sent (Notebook) didn’t amount to the minimum expected read count for a number…

Data Received - Manila clam Supplemental sRNA-seq Data from Azenta

2024

sRNA-seq

Manila clam

Ruditapes philippinarum

30-1035633055

30-1035633055-TS01

Data Received

Received WGBS data for Chris’ Psomagen Project AN00021156.

Data Received - Mytilus trossulus WGBS Data from Psomagen

2024

Mytilus trossulus

bay mussel

WGBS

Psomagen

AN00021156

BS-seq

bisulfite sequencing

Data Received

Daily Bits - November 2024

2024

Daily Bits

Installed RepeatMasker on Raven (GitHub Issue). Installed with dfam38_full.0.h5 repeats partition/database. Deatils on the database here…

<<<<<<< HEAD

=======

Received supplemental sRNA-seq data for Azenta Project 30-1035633055, since the previous data sent (Notebook) didn’t amount to the minimum expected read count for a number…

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Received - Manila clam Supplemental sRNA-seq Data from Azenta

2024

sRNA-seq

Manila clam

Ruditapes philippinarum

30-1035633055

30-1035633055-TS01

Data Received

Received WGBS data for Chris’ Psomagen Project AN00021156.

Data Received - Mytilus trossulus WGBS Data from Psomagen

2024

Mytilus trossulus

bay mussel

WGBS

Psomagen

AN00021156

BS-seq

bisulfite sequencing

Data Received

This notebook consists of a markdown rendering of 01-GO-to-GOslim.Rmd (commit: 351b2ad).

Data Wrangling - Get GOslims from GO IDs for Graces Pycnopodia helianthoides Project

2024

Pycnopodia helianthoides

sunflower sea star

gene ontology

GOslim

data wrangling

Oct 30, 2024

This notebook consists of a markdown rendering of 01-GO-to-GOslim.Rmd (commit: 351b2ad).

<<<<<<< HEAD

Oct 30, 2024

Steven asked that I isolate gDNA from a subset of lake trout (S.namaycush) liver samples (GitHub Issue).

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Isolation Quantification and Gel - Lake Trout Liver Samples

2024

DNA isolation

Qubit

DNA quantification

agarose gel

lake trout

Salvelinus namaycush

liver

Oct 25, 2024

Steven asked that I isolate gDNA from a subset of lake trout (S.namaycush) liver samples (GitHub Issue).

<<<<<<< HEAD

Oct 25, 2024

Continuing with Ariana’s request to extract RNA and run qPCRs (GitHub Issue) for the lifestage_carryover project (GitHub repo), I performed reverse transcription on RNA I…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Reverse Transcription - C.gigas Lifestage Carryover RNA

2024

reverse transcription

cDNA

GoScript

Crassostrea gigas

Pacific oyster

RNA

project-gigas-carryover

lifestage_carryover

Oct 24, 2024

Continuing with Ariana’s request to extract RNA and run qPCRs (GitHub Issue) for the lifestage_carryover project (GitHub repo), I performed reverse transcription on RNA I…

<<<<<<< HEAD

Oct 24, 2024

We recently purchased a 16TB OWC ThunderBlade X8 as additional storage for Raven (Ubuntu 18.04LTS), primarily to be used for Shelly and Emma’s project. Although I thought…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Computer Management - Configure 16TB OWC ThunderBlade X8 External HDD on Raven

2024

Computer Management

HDD

Oct 21, 2024

We recently purchased a 16TB OWC ThunderBlade X8 as additional storage for Raven (Ubuntu 18.04LTS), primarily to be used for Shelly and Emma’s project. Although I thought…

<<<<<<< HEAD

Oct 21, 2024

The original _Salvelinus namaycush C1q bisulfite PCR on 20240911 (Notebook) using bisulfite primers designed on 20240729 (Notebook) failed to produce any amplification. In…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

PCR - Lake Trout C1q Primers with Bisulfite-treated gDNA

2024

C1q

Lake trout

Salvelinus namaycush

PCR

bisulfite

gDNA

liver

gel

Oct 9, 2024

The original _Salvelinus namaycush C1q bisulfite PCR on 20240911 (Notebook) using bisulfite primers designed on 20240729 (Notebook) failed to produce any amplification. In…

<<<<<<< HEAD

Oct 9, 2024

This notebook entry is knitted from urol-e5/timeseries_molecular/D-Apul/code/02.10-D-Apul-RNAseq-genome-index-HiSat2.Rmd (GitHub), commit da11371.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genome Indexing - A.pulchra Genome Using HISAT2

2024

coral

Acropora pulchra

<<<<<<< HEAD

=======

HISAT2 >>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

timeseries_molecular

<<<<<<< HEAD

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

This notebook entry is knitted from urol-e5/timeseries_molecular/D-Apul/code/02.10-D-Apul-RNAseq-genome-index-HiSat2.Rmd (GitHub), commit da11371.

<<<<<<< HEAD

This notebook entry is knitted from urol-e5/timeseries_molecular/D-Apul/code/02.20-D-Apul-RNAseq-alignment-HiSat2.Rmd (GitHub), commit 0f801c0.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA-seq Alignment - A.pulchra RNA-seq Alignments Using HISAT2 and StringTie for Azenta Project 30-1047560508

2024

30-1047560508

RNA-seq

timeseries_molecular

HISAT2

StringTie

alignment

Acropora pulchra

coral

This notebook entry is knitted from urol-e5/timeseries_molecular/D-Apul/code/02.00-D-Apul-RNAseq-gff-to-gtf.Rmd (GitHub), commit cf654b9.

Data Wrangling - Generate GTF from A.pulchra Genome GFF Using gffread

2024

coral

Acropora pulchra

genome

GFF

GTF

gffread

timeseries_molecular

This Rmd file trims A.pulchra RNA-seq files using fastp (Chen 2023), followed by quality checks with FastQC and MultiQC (Ewels et al. 2016).

FastQC Trimming and QC - A.pulchra RNA-seq from Azenta Project 30-1047560508 Using fastp

2024

RNA-seq

30-1047560508

Azenta

coral

Acropora pulchra

fastp

FastQC

MultiQC

trimming

timeseries_molecular

Oct 5, 2024

This Rmd file trims A.pulchra RNA-seq files using fastp (Chen 2023), followed by quality checks with FastQC and MultiQC (Ewels et al. 2016).

<<<<<<< HEAD

Oct 5, 2024

This notebook entry is knitted from urol-e5/timeseries_molecular/D-Apul/code/00.00-D-Apul-RNAseq-reads-FastQC-MultiQC.Rmd (GitHub), commit b7a80be.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

FastQ QC - A.pulchra RNA-seq from Azenta Project 30-1047560508

2024

RNA-seq

30-1047560508

Azenta

coral

Acropora pulchra

FastQC

MultiQC

timeseries_molecular

Oct 4, 2024

This notebook entry is knitted from urol-e5/timeseries_molecular/D-Apul/code/00.00-D-Apul-RNAseq-reads-FastQC-MultiQC.Rmd (GitHub), commit b7a80be.

<<<<<<< HEAD

Oct 4, 2024

Downloaded updated RNA-seq data, from Azenta, which was previously incomplete.

Daily Bits - October 2024

2024

Daily Bits

The sRNA-seq data from Mac’s Manila clam egg samples submitted on 20240722 (Notebook) became available today. Data was downloaded to Owl and is available here:

Data Received - R.philippinarum (Manilla clam) sRNA-seq Data from Azenta Project 30-1035633055

2024

Data Received

sRNA-seq

30-1035633055

Ruditapes philippinarum

Manila clam

The sRNA-seq data from Mac’s Manila clam egg samples submitted on 20240722 (Notebook) became available today. Data was downloaded to Owl and is available here:

<<<<<<< HEAD

Downloaded updated RNA-seq data, from Azenta, which was previously incomplete.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Daily Bits - October 2024

2024

Daily Bits

Coral time series RNA-seq data for Azenta project 30-1047560508 became availalbe today. Data was downloaded to nigthingales on Owl and MD5 checksums were verified.

Data Received - E5 Coral Time Series RNA-seq Azenta Project 30-1047560508

2024

coral

RNA-seq

30-1047560508

Azenta

Data Received

Sep 26, 2024

Coral time series RNA-seq data for Azenta project 30-1047560508 became availalbe today. Data was downloaded to nigthingales on Owl and MD5 checksums were verified.

<<<<<<< HEAD

Sep 26, 2024

After a previous attempt at amplifying the C1q gene in bisulfite-converted DNA failed, we decided we should test out a standard PCR on untreated liver gDNA. I designed PCR…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Agarose Gel - gDNA Integrity Check of Lake Trout Liver gDNA from 20240712

2024

agarose gel

gDNA

Lake trout

liver

Salvelinus namaycush

Sep 25, 2024

After a previous attempt at amplifying the C1q gene in bisulfite-converted DNA failed, we decided we should test out a standard PCR on untreated liver gDNA. I designed PCR…

<<<<<<< HEAD

Sep 25, 2024

After a previous attempt at amplifying the C1q gene in bisulfite-converted DNA failed, we decided we should test out a standard PCR on untreated liver gDNA. I designed PCR…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

PCR - Lake Trout C1Q with Liver gDNA

2024

PCR

Lake trout

C1q

CFX Connect

EpiMark Hot Start Taq

gDNA

liver

Salvelinus namaycush

Sep 24, 2024

After a previous attempt at amplifying the C1q gene in bisulfite-converted DNA failed, we decided we should test out a standard PCR on untreated liver gDNA. I designed PCR…

<<<<<<< HEAD

Sep 24, 2024

This notebook describes using Primer3 (Untergasser et al. 2012; Koressaar and Remm 2007) to reproducibly design primers for sequencing of the lake trout (S.namaycush) (Wikipe…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Primer Design - Lake Trout C1q Gene Sequencing Primers Using Primer3

2024

C1q

lake trout

Salvelinus namaycush

Primer3

primer design

EMBOSS

pyfaidx

Sep 16, 2024

This notebook describes using Primer3 (Untergasser et al. 2012; Koressaar and Remm 2007) to reproducibly design primers for sequencing of the lake trout (S.namaycush) (Wikipe…

<<<<<<< HEAD

Sep 16, 2024

After previously designing bisulfite PCR primers for the C1Q gene on 20240709, and then screwing up the initial PCR, it was time to redo this the correct way. Due to their…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Bisulfite PCR - Second Primer Annealing Gradient Test with Lake Trout Bisulfite-treated DNA

2024

bisulfite

BS-PCR

PCR

DNA

Lake troute

Salvelinus namaycush

Sep 11, 2024

After previously designing bisulfite PCR primers for the C1Q gene on 20240709, and then screwing up the initial PCR, it was time to redo this the correct way. Due to their…

<<<<<<< HEAD

Sep 11, 2024

We’d previously received RNA-seq data from Azenta on 2024-02-21. However, Laura realized that there was a large discrepancy between the amount of reads returned between…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Received - G.macrocephalus Supplemental RNA-seq Data from Azenta Project 30-943133806

Data Received

2024

Gadus macrocephalus

Pacific cod

RNA-seq

Azenta

Sep 9, 2024

We’d previously received RNA-seq data from Azenta on 2024-02-21. However, Laura realized that there was a large discrepancy between the amount of reads returned between…

<<<<<<< HEAD

Sep 9, 2024

Confirmed MD5s for supplemental Pacific cod RNA-seq (Notebook).

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Daily Bits - September 2024

Daily Bits

2024

Sep 3, 2024

Confirmed MD5s for supplemental Pacific cod RNA-seq (Notebook).

<<<<<<< HEAD

Sep 3, 2024

Continued some testing samples for the Pacific cod project. In this instance, Steven and Laura asked that I extract DNA and RNA from the same blood sample (GitHub Issue).…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA and RNA Isolations - Gadus macrocephalus Blood

2024

DNA isolation

RNA isolation

Gadus macrocephalus

Pacific cod

blood

Zymo Quick-DNA/RNA Miniprep

Qubit 3.0

Qubit DNA BR Assay

Qubit RNA HS Assay

Aug 29, 2024

Continued some testing samples for the Pacific cod project. In this instance, Steven and Laura asked that I extract DNA and RNA from the same blood sample (GitHub Issue).…

<<<<<<< HEAD

Aug 29, 2024

This PCR was done incorrectly! The cycling program was setup incorrectly. Notebook post is being left for posterity.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Bisulfite PCR - Testing Primer Annealing Gradient with Lake Trout Bisulfite-treated DNA

2024

BS-PCR

bisulfite

PCR

DNA

Lake trout

Salvelinus namaycush

Aug 28, 2024

This PCR was done incorrectly! The cycling program was setup incorrectly. Notebook post is being left for posterity.

<<<<<<< HEAD

Aug 28, 2024

After isolating gDNA on 20240712 (Notebook), the next step was to perform bisulfite conversion.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Bisulfite Conversion - Lake Trout gDNA Using EZ DNA Methylation Lightning Kit

2024

lake trout

Salvelinus namaycush

bisulfite

EZ DNA Methylation Lightning Kit

Aug 13, 2024

After isolating gDNA on 20240712 (Notebook), the next step was to perform bisulfite conversion.

<<<<<<< HEAD

Aug 13, 2024

Reviewed lab safety inspection report. Fixed some deficiencies.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Daily Bits - August 2024

2024

Daily Bits

Aug 1, 2024

Reviewed lab safety inspection report. Fixed some deficiencies.

<<<<<<< HEAD

Aug 1, 2024

This notebook describes using Primer3 (Untergasser et al. 2012; Koressaar and Remm 2007) to reproducibly design primers for sequencing of the lake trout (S.namaycush) (Wikipe…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Primer Design - Lake Trout C1q Gene Bisulfite Sequencing Primers Using Primer3

2024

C1q

lake trout

Salvelinus namaycush

Primer3

primer design

Jul 29, 2024

This notebook describes using Primer3 (Untergasser et al. 2012; Koressaar and Remm 2007) to reproducibly design primers for sequencing of the lake trout (S.namaycush) (Wikipe…

<<<<<<< HEAD

Jul 29, 2024

Submitted the Manila clam egg samples Mac provided on 20240604 to Azenta for sRNA-seq.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Samples Submitted - Macs Manilla Clam Egg Samples for sRNA-seq at Azenta

2024

Samples Submitted

Azenta

sRNA-seq

Manila clam

Lajonkairia lajonkairii

Ruditapes philippinarum

eggs

Jul 22, 2024

Submitted the Manila clam egg samples Mac provided on 20240604 to Azenta for sRNA-seq.

<<<<<<< HEAD

Jul 22, 2024

Steven asked that I isolate gDNA from a Pacific cod blood samples (GitHub Issue). As we haven’t isolated gDNA from blood before, Laura Spencer identified a set of samples…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Isolation Quantification and Integrity Assessment - Pacific Cod Blood Samples Test

2024

Pacific cod

Gadus macrocephalus

DNA isolation

DNA quantification

Qubit

DNA BR Assay

agarose gel

Steven asked that I isolate gDNA from a Pacific cod blood samples (GitHub Issue). As we haven’t isolated gDNA from blood before, Laura Spencer identified a set of samples…

<<<<<<< HEAD

Steven asked that I isolate gDNA from a Pacific cod blood samples (GitHub Issue). Laura Spencer identified a set of samples (GitHub Issue). Below is the list of samples I…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Isolation and Quantification - Pacific Cod Blood

2024

Pacific cod

Gadus macrocephalus

blood

DNA isolation

DNA quantification

Qubit

DNA BR assay

Steven asked that I isolate gDNA from a Pacific cod blood samples (GitHub Issue). Laura Spencer identified a set of samples (GitHub Issue). Below is the list of samples I…

<<<<<<< HEAD

Steven asked that I isolate gDNA from a subset of lake trout (S.namaycush) liver samples (GitHub Issue) to use for targeted DNA methylation analyses via qPCR.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Isolation and Quantification - Lake Trout Liver

DNA isolation

2024

lake trout

Salvelinus namaycush

Qubit

DNA BR assay

Jul 12, 2024

Steven asked that I isolate gDNA from a subset of lake trout (S.namaycush) liver samples (GitHub Issue) to use for targeted DNA methylation analyses via qPCR.

<<<<<<< HEAD

Jul 12, 2024

I retrieved histology slides (and cassettes) from the UW histology facility for Mac

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Samples Received - L.staminea Histology Slides for Mac

2024

Leukoma staminea

littleneck clam

histology

slides

Samples Received

Jul 9, 2024

I retrieved histology slides (and cassettes) from the UW histology facility for Mac

<<<<<<< HEAD

Jul 9, 2024

Took care of some administrative tasks related to tomorrow’s EH&S Lab Safety Inspection.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Daily Bits - July 2024

2024

Daily Bits

Took care of some administrative tasks related to tomorrow’s EH&S Lab Safety Inspection.

<<<<<<< HEAD

I was asked to isolate RNA from a list of samples (GitHub Issue) from a number of Crassostrea gigas (Pacific oyster) spat, seed, and adults that had been collected as part…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation and Quantification - C.gigas Lifestage Carryover Seed Juvenile and Adult

2024

project-lifestage-carryover

Crassostrea gigas

Pacific oyster

seed

adult

juvenile

RNA HS assay

Qubit

RNA isolation

RNA quantification

Directzol RNA miniprep

I was asked to isolate RNA from a list of samples (GitHub Issue) from a number of Crassostrea gigas (Pacific oyster) spat, seed, and adults that had been collected as part…

<<<<<<< HEAD

I was asked to isolate RNA from a list of samples (GitHub Issue) from a number of Crassostrea gigas (Pacific oyster) spat, seed, and adults that had been collected as part…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation and Quantification - C.gigas Lifestage Carryover Seed Juvenile and Adult

2024

project-lifestage-carryover

Crassostrea gigas

Pacific oyster

seed

adult

juvenile

RNA HS assay

Qubit

RNA isolation

Directzol RNA Miniprep

Jun 28, 2024

I was asked to isolate RNA from a list of samples (GitHub Issue) from a number of Crassostrea gigas (Pacific oyster) spat, seed, and adults that had been collected as part…

<<<<<<< HEAD

Jun 28, 2024

I was asked to isolate RNA from a list of samples (GitHub Issue) from a number of Crassostrea gigas (Pacific oyster) spat, seed, and adults that had been collected as part…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation and Quantification - C.gigas Lifestage Carryover Seed Juvenile and Adult

2024

project-lifestage-carryover

Crassostrea gigas

Pacific oyster

seed

adult

juvenile

RNA HS assay

Qubit

RNA isolation

Directzol RNA Miniprep

Jun 27, 2024

I was asked to isolate RNA from a list of samples (GitHub Issue) from a number of Crassostrea gigas (Pacific oyster) spat, seed, and adults that had been collected as part…

<<<<<<< HEAD

Jun 27, 2024

I was asked to isolate RNA from a list of samples (GitHub Issue) from a number of Crassostrea gigas (Pacific oyster) spat, seed, and adults that had been collected as part…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation and Quantification - C.gigas Lifestage Carryover Seed Juvenile and Adult

2024

project-lifestage-carryover

Crassostrea gigas

Pacific oyster

seed

adult

juvenile

RNA HS assay

Qubit

RNA isolation

Directzol RNA Miniprep

Jun 26, 2024

I was asked to isolate RNA from a list of samples (GitHub Issue) from a number of Crassostrea gigas (Pacific oyster) spat, seed, and adults that had been collected as part…

<<<<<<< HEAD

Jun 26, 2024

I was asked to isolate RNA from a list of samples (GitHub Issue) from a number of Crassostrea gigas (Pacific oyster) spat, seed, and adults that had been collected as part…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation and Quantification - C.gigas Lifestage Carryover Seed Juvenile and Adult

2024

project-lifestage-carryover

Crassostrea gigas

Pacific oyster

seed

adult

juvenile

RNA HS assay

Qubit

RNA isolation

Directzol RNA Miniprep

Jun 25, 2024

I was asked to isolate RNA from a list of samples (GitHub Issue) from a number of Crassostrea gigas (Pacific oyster) spat, seed, and adults that had been collected as part…

<<<<<<< HEAD

Jun 25, 2024

I was asked to isolate RNA from a list of samples (GitHub Issue) from a number of Crassostrea gigas (Pacific oyster) spat, seed, and adults that had been collected as part…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation and Quantification - C.gigas Lifestage Carryover Seed Juvenile and Adult

2024

project-gigas-carryover

Crassostrea gigas

Pacific oyster

adult

seed

spat

Directzol RNA Miniprep

Qubit

RNA HS Assay

I was asked to isolate RNA from a list of samples (GitHub Issue) from a number of Crassostrea gigas (Pacific oyster) spat, seed, and adults that had been collected as part…

<<<<<<< HEAD

Sent bad Gannet HDD identified on 20240616 back to Amazon vendor (Maestro Technologies), using the supplied RMA shipping label. Drive will be replaced at their cost.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

HDD RMA - Failed Gannet HDD from 20240615

gannet

HDD

Synology

Sent bad Gannet HDD identified on 20240616 back to Amazon vendor (Maestro Technologies), using the supplied RMA shipping label. Drive will be replaced at their cost.

<<<<<<< HEAD

I was asked to isolate RNA from a list of samples (GitHub Issue) from a number of Crassostrea gigas (Pacific oyster) spat, seed, and adults that had been collected as part…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation and Quantification - C.gigas Lifestage Carryover Seed Juvenile and Adult

2024

project-gigas-carryover

Crassostrea gigas

Pacific oyster

adult

seed

spat

Directzol RNA Miniprep

Qubit

RNA HS assay

I was asked to isolate RNA from a list of samples (GitHub Issue) from a number of Crassostrea gigas (Pacific oyster) spat, seed, and adults that had been collected as part…

<<<<<<< HEAD

Mac requested I dop off some littleneck clam histology cassettes (GitHub Issue) at the UW Pathology Research Services Laboratory (HSB C411).

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Samples Submitted - Littleneck Clam Histology Cassettes to UW Pathology Research Services Laboratory

2024

histology

littleneck clam

Pathology Research Services Laboratory

Samples Submitted

Mac requested I dop off some littleneck clam histology cassettes (GitHub Issue) at the UW Pathology Research Services Laboratory (HSB C411).

<<<<<<< HEAD

I was asked to isolate RNA from a list of samples (GitHub Issue) from a number of Crassostrea gigas (Pacific oyster) spat, seed, and adults that had been collected as part…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation - C.gigas Lifestage Carryover Seed Juvenile and Adult

2024

project-gigas-carryover

Directzol RNA Miniprep

<<<<<<< HEAD

=======

Crassostrea gigas

Pacific oyster

seed

adult

juvenile

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Jun 17, 2024

I was asked to isolate RNA from a list of samples (GitHub Issue) from a number of Crassostrea gigas (Pacific oyster) spat, seed, and adults that had been collected as part…

<<<<<<< HEAD

Jun 17, 2024

I was asked to isolate RNA from a list of samples (GitHub Issue) from a number of Crassostrea gigas (Pacific oyster) spat, seed, and adults that had been collected as part…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Quantification - C.gigas RNA Lifestage Carryover from 20240615 and 20240617

2024

project-gigas-carryover

Crassostrea gigas

Pacific oyster

seed

adult

juvenile

Qubit

RNA HS assay

Jun 17, 2024

I was asked to isolate RNA from a list of samples (GitHub Issue) from a number of Crassostrea gigas (Pacific oyster) spat, seed, and adults that had been collected as part…

RNA Isolation - C.gigas Lifestage Carryover Seed Juvenile and Adult

2024

project-gigas-carryover

Directzol RNA Miniprep

Crassostrea gigas

Pacific oyster

seed

adult

juvenile

I was asked to isolate RNA from a list of samples (GitHub Issue) from a number of Crassostrea gigas (Pacific oyster) spat, seed, and adults that had been collected as part…

<<<<<<< HEAD

Hard drive recently failed (showed “Critical” status in Synology Storage Manager). Replaced the drive with a new one. Checking the serial number on Seagate’s website…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Computer Maintenance - Replace Bad HDD on Gannet

computer maintenance

2024

HDD

gannet

synology

Hard drive recently failed (showed “Critical” status in Synology Storage Manager). Replaced the drive with a new one. Checking the serial number on Seagate’s website…

<<<<<<< HEAD

Differential gene expression of 9^oC vs 16^oC liver RNA-seq using edgeR (Chen et al. 2024; McCarthy, Chen, and Smyth 2012; Chen, Lun, and Smyth 2016; Robinson, McCarthy, and…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Differential Gene Expression - G.macrocephalus RNA-seq 9C vs 16C Using edgeR

edgeR

Pacific cod

RNA-seq

differential gene expression

2024

Gadus macrocephalus

Jun 11, 2024

Differential gene expression of 9^oC vs 16^oC liver RNA-seq using edgeR (Chen et al. 2024; McCarthy, Chen, and Smyth 2012; Chen, Lun, and Smyth 2016; Robinson, McCarthy, and…

<<<<<<< HEAD

Jun 11, 2024

Went to NOAA (NWFSC) to get Manilla clam (Lajonkairia lajonkairii) egg samples from Mac for an RNA-seq project.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Samples Received - Lajonkairia lajonkairii Egg Samples from Mackenzie Gavery

Lajonkairia lajonkairii

manilla clam

2024

Samples Received

Jun 4, 2024

Went to NOAA (NWFSC) to get Manilla clam (Lajonkairia lajonkairii) egg samples from Mac for an RNA-seq project.

<<<<<<< HEAD

Jun 4, 2024

Isolated and quantified RNA (Notebook) for `project-lifestage-carryover project (GitHub repo).

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Daily Bits - June 2024

Daily Bits

2024

Jun 1, 2024

Isolated and quantified RNA (Notebook) for `project-lifestage-carryover project (GitHub repo).

<<<<<<< HEAD

Jun 1, 2024

Previously isolated and quantified gDNA on 20240531 (Notebook) and needed to evaluate gDNA integrity. We recently sent a bunch of liver samples off to Psomagagen for whole…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Agarose Gel - G.macrocephalus gDNA from 20240521

agarose

gDNA

Gadus macrocephalus

Pacific cod

gel

2024

May 31, 2024

Previously isolated and quantified gDNA on 20240531 (Notebook) and needed to evaluate gDNA integrity. We recently sent a bunch of liver samples off to Psomagagen for whole…

<<<<<<< HEAD

May 31, 2024

We recently sent a bunch of liver samples off to Psomagagen for whole genome bisulfite sequencing (WGBS). As documented in this GitHub Issue, Psomagen discovered that the…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Isolation - Pacific cod liver

DNA isolation

Pacific cod

liver

Gadus macrocephalus

DNA quantification

Qubit

2024

May 21, 2024

We recently sent a bunch of liver samples off to Psomagagen for whole genome bisulfite sequencing (WGBS). As documented in this GitHub Issue, Psomagen discovered that the…

<<<<<<< HEAD

May 21, 2024

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Daily Bits - May 2024

Daily Bits

2024

Ran G.macrocephalus gDNA on a gel.

May 1, 2024

Ran G.macrocephalus gDNA on a gel.

<<<<<<< HEAD

May 1, 2024

Submitted 40 Gadus macrocephalus tissue/blood samples (GitHub Issue) to Psomagen for gDNA isolation and whole genome bisulfite sequencing (WGBS).

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Samples Submitted - Pacific Cod 40 Tissue Samples for WGBS at Psomagen

psomagen

WGBS

2024

Pacific cod

Gadus macrocephalus

BS-seq

bisulfite

Samples Submitted

Apr 30, 2024

Submitted 40 Gadus macrocephalus tissue/blood samples (GitHub Issue) to Psomagen for gDNA isolation and whole genome bisulfite sequencing (WGBS).

<<<<<<< HEAD

Apr 30, 2024

Most of this stuff is addressed in this GitHub Issue, but here’s the summary:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Computer Troubleshooting - Gannet Missing Storage Pool

gannet

Synology

server

2024

Apr 23, 2024

Most of this stuff is addressed in this GitHub Issue, but here’s the summary:

<<<<<<< HEAD

Apr 23, 2024

Helped Eric get started with qPCR analysis.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Daily Bits - April 2024

daily bits

2024

Apr 1, 2024

Helped Eric get started with qPCR analysis.

<<<<<<< HEAD

Apr 1, 2024

qPCR analysis of Crassostrea gigas (Pacific oyster) spat and seed from the project-gigas-carryover (GitHub Repo).

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR Analysis - C.gigas Lifestages Carryover from 20240325

2024

qPCR

Crassotrea gigas

Pacific oyster

Mar 27, 2024

qPCR analysis of Crassostrea gigas (Pacific oyster) spat and seed from the project-gigas-carryover (GitHub Repo).

<<<<<<< HEAD

Mar 27, 2024

Ran qPCRs on the cDNA I made last week (Notebook), as part of the project-gigas-carryover (GitHub Repo). This file provides metadata for the samples being qPCR’d:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCRs - C.gigas Lifestage Carryover cDNA

qPCR

SsoFast

CFX Connect

HSP70

HSP90

GAPDH

VIPERIN

ATPsynthase

cGAS

DMNT1

citrate synthase

Crassostrea gigas

Pacific oyster

cDNA

Mar 25, 2024

Ran qPCRs on the cDNA I made last week (Notebook), as part of the project-gigas-carryover (GitHub Repo). This file provides metadata for the samples being qPCR’d:

<<<<<<< HEAD

Mar 25, 2024

I was asked to isolate RNA from a list of samples (GitHub Issue) from a number of Crassostrea gigas (Pacific oyster) spat and seed that had been collected as part of the proj…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation - C.gigas Lifestage Carryover Seed and Spat

RNA isolation

Crassostrea gigas

Lifestage carryover

<<<<<<< HEAD

=======

Pacific oyster

2024

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Mar 19, 2024

I was asked to isolate RNA from a list of samples (GitHub Issue) from a number of Crassostrea gigas (Pacific oyster) spat and seed that had been collected as part of the proj…

<<<<<<< HEAD

Mar 19, 2024

After isolating RNA earlier today (Notebook) for the project-gigas-carryover/lifestage_carryover (GitHub repo), I proceeded with reverse transcription for those samples with…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Reverse Transcription - C.gigas Lifestage Carryover Seed and Spat

reverse transcription

Lifestage carryover

Crassostrea gigas

Pacific oyster

cDNA

M-MLV

2024

Mar 19, 2024

Finally got around to getting the CEABIGR (GitHub repo) sequencing data uploaded to NCBI’s Short Read Archive (SRA). Data transfer took quite awhile, as we have both whole…

SRA Submission - CEABIGR WGBS and RNA-seq

SRA

CEABIGR

Crassostrea virginica

Eastern oyster

RNAseq

WGBS

2024

Mar 18, 2024

Finally got around to getting the CEABIGR (GitHub repo) sequencing data uploaded to NCBI’s Short Read Archive (SRA). Data transfer took quite awhile, as we have both whole…

<<<<<<< HEAD

Mar 18, 2024

After running the initial resazuring test on 20240308 (Notebook), Steven/Ariana asked that I run another trial (GitHub Issue). This second trial was designed to get some…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Resazurin - C.gigas Second Trial

Crassostrea gigas

Pacific oyster

2024

resazurin

Mar 12, 2024

After running the initial resazuring test on 20240308 (Notebook), Steven/Ariana asked that I run another trial (GitHub Issue). This second trial was designed to get some…

<<<<<<< HEAD

Mar 12, 2024

We’re beginning to gather some preliminary data for a project examining the effects of “stress priming” on _Crassostrea gigas (Pacific oyster). GitHub repo is here. As part…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Resazurin - Preliminary Respiration Test Using C.gigas

resazurin

Crassostrea gigas

Pacific oyster

2024

Mar 8, 2024

We’re beginning to gather some preliminary data for a project examining the effects of “stress priming” on _Crassostrea gigas (Pacific oyster). GitHub repo is here. As part…

<<<<<<< HEAD

Mar 8, 2024

Isolated RNA for gigas carryover project (Notebook)

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Daily Bits - March 2024

2024

Daily Bits

Mar 1, 2024

Isolated RNA for gigas carryover project (Notebook)

<<<<<<< HEAD

Mar 1, 2024

Received Pacific cod liver/gill/spleen RNA-seq data back from Azenta today (project 30-943133806). Files were downloaded to Owl and MD5 checksums were verified. The Nightinga…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Received - Pacific cod RNA-seq Azenta Project 30-943133806

Azenta

RNA-seq

2024

Pacific cod

Gadus macrocephalus

30-943133806

Data Received

Feb 21, 2024

Received Pacific cod liver/gill/spleen RNA-seq data back from Azenta today (project 30-943133806). Files were downloaded to Owl and MD5 checksums were verified. The Nightinga…

<<<<<<< HEAD

Feb 21, 2024

Our previous sRNA-seq data analysis for this project revealed that the R2 reads didn’t seem to match with anything (specifically, no clade assignments when using miRTrace)…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

sRNA-seq Paired Read Merging Explorations - Coral E5 Deep Dive

2024

sRNA-seq

merge

bbmerge

fastp

Feb 2, 2024

Our previous sRNA-seq data analysis for this project revealed that the R2 reads didn’t seem to match with anything (specifically, no clade assignments when using miRTrace)…

<<<<<<< HEAD

Feb 2, 2024

Finalized females/males controls/exposed expression table.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Daily Bits - February 2024

2024

Daily Bits

Feb 1, 2024

Finalized females/males controls/exposed expression table.

<<<<<<< HEAD

Feb 1, 2024

As part of the CEABIGR project (GitHub repo) Steven performed some inital data wrangling to test out the basic calculations to determine the natural log of the fold change…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Figure Updates - CEABIGR Spurious Transcription Calcs and Plotting Using Exon Sum Threshold

CEABIGR

2024

plot

Eastern oyster

Crassostrea virginica

Jan 24, 2024

As part of the CEABIGR project (GitHub repo) Steven performed some inital data wrangling to test out the basic calculations to determine the natural log of the fold change…

<<<<<<< HEAD

Jan 24, 2024

As part of the CEABIGR project (GitHub repo) Steven performed some inital data wrangling to test out the basic calculations to determine the natural log of the fold change…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Exploration - CEABIGR Spurious Transcription Calculations and Plotting

2024

CEABIGR

plot

Eastern oyster

Crassostrea virginica

Jan 3, 2024

As part of the CEABIGR project (GitHub repo) Steven performed some inital data wrangling to test out the basic calculations to determine the natural log of the fold change…

<<<<<<< HEAD

Jan 3, 2024

Helped Chris troubleshoot her SOD assay standard curve. She felt like her samples SOD activity was too low and falling outside of the standard curve.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Daily Bits - January 2024

2024

Daily Bits

Jan 2, 2024

Helped Chris troubleshoot her SOD assay standard curve. She felt like her samples SOD activity was too low and falling outside of the standard curve.

<<<<<<< HEAD

Jan 2, 2024

After replacing the three failing HDDs in the Gannet (Synology) expansion unit, I contacted the company (Maestro Technology LLC) via Amazon. They have been very responsive…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Computer Management - Returned Failing HDDs from Gannet Expansion Unit

computer management

2023

HDDs

gannet

Dec 21, 2023

After replacing the three failing HDDs in the Gannet (Synology) expansion unit, I contacted the company (Maestro Technology LLC) via Amazon. They have been very responsive…

<<<<<<< HEAD

Dec 21, 2023

Shipped box of 80 Pacific cod tissues selected by Steven (mostly liver, some blood, gills, and spleen) to Azenta overnight on dry ice for RNA-seq.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Samples Submitted - Gadus macrocephalus liver tissues to Azenta for RNA-seq

2023

Gadus macrocephalus

Pacific cod

Azenta

RNA-seq

Samples Submitted

liver

spleen

gill

blood

Dec 18, 2023

Shipped box of 80 Pacific cod tissues selected by Steven (mostly liver, some blood, gills, and spleen) to Azenta overnight on dry ice for RNA-seq.

<<<<<<< HEAD

Dec 18, 2023

In mid-Novemeber, our Synology RX1217 expansion unit on Gannet generated erros for three drives. Considering this unit, and the corresponding HDDs, were installed in July…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Computer Maintenance - Replace Failing HDDs in Synology RX1217 Expansion Unit on Gannet

gannet

synology

RX1217

HDDs

2023

computer maintenance

Dec 7, 2023

In mid-Novemeber, our Synology RX1217 expansion unit on Gannet generated erros for three drives. Considering this unit, and the corresponding HDDs, were installed in July…

<<<<<<< HEAD

Dec 7, 2023

After Steven ran through some prelimiary exon expression analyses (GitHub Isse), he noticed that there were some genes with a seemingly excessive number of exons (like over…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Investigation - Mysterious Case of Excessive Exons in CEABIGR

CEABIGR

Crassostrea viriginica

Eastern oyster

2023

Dec 6, 2023

After Steven ran through some prelimiary exon expression analyses (GitHub Isse), he noticed that there were some genes with a seemingly excessive number of exons (like over…

<<<<<<< HEAD

Dec 6, 2023

Read Ch.3 of “Race After Technology: The New Jim Code”

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Daily Bits - December 2023

Daily Bits

Dec 1, 2023

Read Ch.3 of “Race After Technology: The New Jim Code”

<<<<<<< HEAD

Dec 1, 2023

For today’s lab meeting, Steven tasked us with the following on Wednesday:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Plotting Fun - Lab Meeting Task

plotting

Nov 30, 2023

For today’s lab meeting, Steven tasked us with the following on Wednesday:

<<<<<<< HEAD

Nov 30, 2023

As part of transcriptome annotation (GitHub issue) for DuMOAR (GitHub repo), I’ve already run TransDecoder ( run on 20231107), as well as DIAMOND BLASTx (run earlier today).…

Transcriptome Annotation - M.magister De Novo Transcriptome Assembly Using Trinotate on Mox

mox

2023

Metacarcinus magister

Dungenss crab

Trinotate

transcriptome

annotation

As part of the process for using Trinotate for transcriptome annotation (GitHub Issue), I previously ran TransDecoder on 20231107. Next, I needed to run BLASTx. As usual, I…

Transcriptome Annotation - M.magister De Novo Transcriptome Assembly for DuMOAR Project Using DIAMOND BLASTx on Mox

mox

DIAMOND

BLASTx

transcriptome

2023

DuMOAR

Dungeness crab

Metacarcinus magister

As part of the process for using Trinotate for transcriptome annotation (GitHub Issue), I previously ran TransDecoder on 20231107. Next, I needed to run BLASTx. As usual, I…

<<<<<<< HEAD

As part of transcriptome annotation (GitHub issue) for DuMOAR (GitHub repo), I’ve already run TransDecoder ( run on 20231107), as well as DIAMOND BLASTx (run earlier today).…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Annotation - M.magister De Novo Transcriptome Assembly Using Trinotate on Mox

mox

2023

Metacarcinus magister

Dungenss crab

Trinotate

transcriptome

annotation

Ran a “quick and dirty” qPCR analysis for the qPCR’s I’d previously run:

Daily Bits - November 2023

Daily Bits

2023

<<<<<<< HEAD

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR Analysis - C.gigas Matt George PolyIC Diploids

qPCR

CFX Connect

Crassostrea gigas

diploid

Pacific oyster

2023

Miscellaneous

Aug 22, 2023

Ran a “quick and dirty” qPCR analysis for the qPCR’s I’d previously run:

<<<<<<< HEAD

Aug 22, 2023

In the process of generating expression matrices for CEABIGR (GitHub repo), and in turn distance matrices for these samples, I realized a couple of things:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcript Identification and Alignments - C.virginica RNAseq with NCBI Genome GCF_002022765.2 Using Hisat2 and Stringtie on Mox Again

hisat2

mox

Crassostrea virginica

stringtie

RNAseq

Eastern oyster

2023

Miscellaneous

Aug 21, 2023

In the process of generating expression matrices for CEABIGR (GitHub repo), and in turn distance matrices for these samples, I realized a couple of things:

<<<<<<< HEAD

Aug 21, 2023

Using diploid MgCl₂ control cDNA from 20230816, performed qPCR on the following primer sets selected by Steven (GitHub Issue), along with Cg_Actin as a potential normalizing…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - C.gigas PolyIC Diploid MgCl2

2023

Miscellaneous

Aug 17, 2023

Using diploid MgCl₂ control cDNA from 20230816, performed qPCR on the following primer sets selected by Steven (GitHub Issue), along with Cg_Actin as a potential normalizing…

<<<<<<< HEAD

Aug 17, 2023

After quantifying diploid MgCl₂ (Notebook) earlier today and proceeded to make cDNA. Reverse transcription was performed using oligo dT primers using M-MLV RT (Promega), per…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Reverse Transcription - C.gigas PolyIC Diploid MgCl2

2023

Miscellaneous

After quantifying diploid MgCl₂ (Notebook) earlier today and proceeded to make cDNA. Reverse transcription was performed using oligo dT primers using M-MLV RT (Promega), per…

<<<<<<< HEAD

Steven asked me to generate cDNA (GitHub Issue) from Crassostrea gigas (Pacific oyster) RNA, as part of Matt George’s polyIC project. I had previously quantified RNA from…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Quantification - C.gigas PolyIC Diploid MgCl2

polyIC

Crassostrea gigas

Pacific oyster

2023

Miscellaneous

Steven asked me to generate cDNA (GitHub Issue) from Crassostrea gigas (Pacific oyster) RNA, as part of Matt George’s polyIC project. I had previously quantified RNA from…

<<<<<<< HEAD

Steven asked that I run ShortStack on the E5 P.evermanni sRNA-seq (GitHub Issue) data we had. I used trimmed sRNA-seq reads from 20230620 (notebook entry) and the P.evermanni…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Daily Bits - August 2023

2023

Daily Bits

<<<<<<< HEAD

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

sRNA-seq Alignments - E5 Coral P.evermanni Using ShortStack on Mox

sRNA

Porites evermanni

ShortStack

mox

2023

Jul 31, 2023

Steven asked that I run ShortStack on the E5 P.evermanni sRNA-seq (GitHub Issue) data we had. I used trimmed sRNA-seq reads from 20230620 (notebook entry) and the P.evermanni…

<<<<<<< HEAD

Jul 31, 2023

After getting Arthropoda and Unassigned reads extracted to FastA format (notebook entry) using MEGAN6 Community Edition, the next step was to use the FastA files to extract…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Read Extractions - M.magister MEGAN FastA to FastQ Arthropoda and Unassigned Reads

Metacarcinus magister

Dungeness crab

MEGAN

2023

DuMOAR

Jul 30, 2023

After getting Arthropoda and Unassigned reads extracted to FastA format (notebook entry) using MEGAN6 Community Edition, the next step was to use the FastA files to extract…

<<<<<<< HEAD

Jul 30, 2023

As part of annotating Ballgown transcripts for this project, I generated a genes FastA file on 20230726 (notebook entry). The next aspect of the annotation process was to…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DIAMOND BLASTx - C.virginica Genes on Mox

2023

CEABIGR

Jul 27, 2023

As part of annotating Ballgown transcripts for this project, I generated a genes FastA file on 20230726 (notebook entry). The next aspect of the annotation process was to…

<<<<<<< HEAD

Jul 27, 2023

Using cDNA from 20230721, performed qPCR on the following primer sets selected by Steven (GitHub Issue), along with Cg_Actin as a potential normalizing gene:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - C.gigas polyIC

2023

Miscellaneous

Using cDNA from 20230721, performed qPCR on the following primer sets selected by Steven (GitHub Issue), along with Cg_Actin as a potential normalizing gene:

<<<<<<< HEAD

I’ve been reviewing some of the CEABIGR (GitHub repo) data I’ve generated; specifically transcript count data/calcs. As part of that, I feel like we need/should annotate the…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Wrangling - C.virginica Genes Only FastA from Genes BED File Using gffread on Raven

2023

CEABIGR

I’ve been reviewing some of the CEABIGR (GitHub repo) data I’ve generated; specifically transcript count data/calcs. As part of that, I feel like we need/should annotate the…

<<<<<<< HEAD

After converting DIAMOND BLASTx/MEGAN DAA files to RMA6 and looking at the taxonomic breakdown of each sample (notebook entry), it was decided we should extract reads from Ar…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Read Extractions - M.magister MEGAN Arthropoda and Unassigned Reads to FastA

Metacarcinus magister

Dungeness crab

MEGAN

2023

DuMOAR

After converting DIAMOND BLASTx/MEGAN DAA files to RMA6 and looking at the taxonomic breakdown of each sample (notebook entry), it was decided we should extract reads from Ar…

<<<<<<< HEAD

Steven asked me to generate cDNA (GitHub Issue) from Crassostrea gigas (Pacific oyster) RNA, as part of Matt George’s polyIC project. Before starting reverse transcription…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Quantification - C.gigas PolyIC

2023

Miscellaneous

Steven asked me to generate cDNA (GitHub Issue) from Crassostrea gigas (Pacific oyster) RNA, as part of Matt George’s polyIC project. Before starting reverse transcription…

<<<<<<< HEAD

Quantified RNA earlier today and proceeded to make cDNA. Reverse transcription was performed using oligo dT primers using M-MLV RT (Promega), per the manufacturer’s…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Reverse Transcription - C.gigas PolyIC RNA

2023

Miscellaneous

Quantified RNA earlier today and proceeded to make cDNA. Reverse transcription was performed using oligo dT primers using M-MLV RT (Promega), per the manufacturer’s…

<<<<<<< HEAD

Using cDNA from 20230713, performed qPCR on the following primer sets selected by Steven:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - C.gigas Ctenidia cDNA for Noah’s Heat-Mechanical Stress Project

2023

Miscellaneous

Using cDNA from 20230713, performed qPCR on the following primer sets selected by Steven:

<<<<<<< HEAD

Using cDNA from 20230713, performed qPCR on the following primer sets selected by Steven:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - C.gigas Ctenidia cDNA for Noah’s Heat-Mechanical Stress Project

2023

Miscellaneous

Jul 19, 2023

Using cDNA from 20230713, performed qPCR on the following primer sets selected by Steven:

<<<<<<< HEAD

Jul 19, 2023

After generating cDNA earlier today from Noah’s Crassostrea gigas (Pacific oyster) RNA (isolated 20230712), I ran qPCRs using the pooled cDNA sample to test out some primers…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - C.gigas cDNA Primer Tests for Noah’s Heat-Mechanical Stress Project

qPCR

Crassostrea gigas

cDNA

Noah

Pacific oyster

2023

After generating cDNA earlier today from Noah’s Crassostrea gigas (Pacific oyster) RNA (isolated 20230712), I ran qPCRs using the pooled cDNA sample to test out some primers…

<<<<<<< HEAD

After isolating ctenidia RNA on 20230712 and then quantifying the RNA earlier today, I needed to perform reverse transcription to have cDNA for subsequent qPCRs. Reverse…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Reverse Transcription - C.gigas RNA from Noah’s Heat-Mechanical Stress Project

reverse transcription

Crassostrea gigas

RNA

Pacific oyster

2023

After isolating ctenidia RNA on 20230712 and then quantifying the RNA earlier today, I needed to perform reverse transcription to have cDNA for subsequent qPCRs. Reverse…

<<<<<<< HEAD

I quantified Noah’s Crassostrea gigas (Pacific oyster) ctenidia RNA from yesterday (20230712) using the Roberts Lab Qubit 3 and the RNA High Sensitivity (HS) Assay. 1uL of…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Quantification - C.gigas RNA from Noah’s Heat-Mechanical Stress Project

2023

Miscellaneous

I quantified Noah’s Crassostrea gigas (Pacific oyster) ctenidia RNA from yesterday (20230712) using the Roberts Lab Qubit 3 and the RNA High Sensitivity (HS) Assay. 1uL of…

<<<<<<< HEAD

Steven asked that I help isolate RNA (GitHub Issue) for Noah’s summer project involving heat and mechanical stress (tumbling) of adult Crassostrea gigas (Pacific oyster).…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation - C.gigas Ctenidia from Noah’s Heat-Mechanical Stress Project

2023

Miscellaneous

Jul 12, 2023

Steven asked that I help isolate RNA (GitHub Issue) for Noah’s summer project involving heat and mechanical stress (tumbling) of adult Crassostrea gigas (Pacific oyster).…

<<<<<<< HEAD

Jul 12, 2023

After the initial DIAMOND BLASTx and subsequent MEGANization(notebook) ran for 41 days, I attempted to open the extremely large files in the MEGAN6 GUI to get an overview of…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Daily Bits - July 2023

2023

Daily Bits

<<<<<<< HEAD

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

File Conversion - M.magister MEGANized DAA to RMA6

megan

DAA

RMA6

Metacarcinus magister

dungeness crab

2023

Miscellaneous

Jul 2, 2023

After the initial DIAMOND BLASTx and subsequent MEGANization(notebook) ran for 41 days, I attempted to open the extremely large files in the MEGAN6 GUI to get an overview of…

<<<<<<< HEAD

Jul 2, 2023

Downloaded Pacific cod (_G.macrocephalus) sequencing data. I believe this is a NOAA project, and I don’t have any info about it. So, not much to report here.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Received - Pacific Cod (G.macrocephalus) Sequencing Data from Novogene

2023

Data Received

Jun 30, 2023

Downloaded Pacific cod (_G.macrocephalus) sequencing data. I believe this is a NOAA project, and I don’t have any info about it. So, not much to report here.

<<<<<<< HEAD

Jun 30, 2023

Steven had asked that I align the coral E5 sRNA-seq reads using ShortStack (GitHub Issue). I previously trimmed the sRNA-seq reads to 35bp in length (notebook). Next up was…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

sRNA-seq Alignments - E5 Coral A.pulchra P.meandrina Using ShortStack on Mox

2023

Jun 28, 2023

Steven had asked that I align the coral E5 sRNA-seq reads using ShortStack (GitHub Issue). I previously trimmed the sRNA-seq reads to 35bp in length (notebook). Next up was…

<<<<<<< HEAD

Jun 28, 2023

After downloading data on 20230515 (notebook) and then reorganizing the E5 coral RNA-seq data from Azenta project 30-789513166 (notebook), and after testing some trimming…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Trimming and QC - E5 Coral sRNA-seq Data fro A.pulchra P.evermanni and P.meandrina Using FastQC flexbar and MultiQC on Mox

flexbar

trimming

FastQC

MultiQC

mox

coral

2023

Jun 20, 2023

After downloading data on 20230515 (notebook) and then reorganizing the E5 coral RNA-seq data from Azenta project 30-789513166 (notebook), and after testing some trimming…

<<<<<<< HEAD

Jun 20, 2023

After performing a de novo transcriptome assembly with L.staminea RNA-seq data, the Trinity assembly stats were quite a bit more “exaggerated” than normally expected. In an…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

ORF Identification - L.staminea De Novo Transcriptome Assembly v1.0 Using Transdecoder on Mox

2023

Miscellaneous

Jun 17, 2023

After performing a de novo transcriptome assembly with L.staminea RNA-seq data, the Trinity assembly stats were quite a bit more “exaggerated” than normally expected. In an…

<<<<<<< HEAD

Jun 17, 2023

As part of this GitHub Issue to create a de novo transcriptome assembly from L.staminea RNA-seq data, I trimmed the reads earlier today. Next up is the actual do novo assembl…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Assembly - De Novo L.staminea Trimmed RNAseq Using Trinity on Mox

2023

Miscellaneous

As part of this GitHub Issue to create a de novo transcriptome assembly from L.staminea RNA-seq data, I trimmed the reads earlier today. Next up is the actual do novo assembl…

<<<<<<< HEAD

Per this GitHub Issue, Steven asked me to perform a de novo transcriptome assembly on one set of paired FastQ from some little neck clam (L.staminea) RNA-seq. Prior to…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Trimming - L.staminea RNA-seq Using FastQC fastp and MultiQC on Mox

2023

Miscellaneous

Per this GitHub Issue, Steven asked me to perform a de novo transcriptome assembly on one set of paired FastQ from some little neck clam (L.staminea) RNA-seq. Prior to…

<<<<<<< HEAD

Steven asked me to run RepeatMasker on the P.meandrina genome (GitHub Issue) for eventual use in developing a count matrix for transposable elements. The P.meandrina genome…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Daily Bits - June 2023

2023

Daily Bits

<<<<<<< HEAD

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Repeats Identification - P.meandrina Using RepeatMasker on Mox

2023

May 26, 2023

Steven asked me to run RepeatMasker on the P.meandrina genome (GitHub Issue) for eventual use in developing a count matrix for transposable elements. The P.meandrina genome…

<<<<<<< HEAD

May 26, 2023

In preparation for FastQC and trimming of the E5 coral sRNA-seq data, I noticed that my “default” trimming settings didn’t produce the results I expected. Specifically…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Trimming and QC - E5 Coral sRNA-seq Trimming Parameter Tests and Comparisons

2023

May 24, 2023

In preparation for FastQC and trimming of the E5 coral sRNA-seq data, I noticed that my “default” trimming settings didn’t produce the results I expected. Specifically…

<<<<<<< HEAD

May 24, 2023

As part of getting P.meandrina genome info added to our Lab Handbook Genomic Resources page, I will index the P.meandrina genome file (Pocillopora_meandrina_HIv1.assembly.fas…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Wrangling - P.meandrina Genome GFF to GTF Using gffread

gffread

jupyter

Pocillopora meandrina

cora

GFF

GTF

2023

As part of getting P.meandrina genome info added to our Lab Handbook Genomic Resources page, I will index the P.meandrina genome file (Pocillopora_meandrina_HIv1.assembly.fas…

<<<<<<< HEAD

After downloading RNA-seq data on 20230516 and then reorganizing the E5 coral RNA-seq data from Azenta project 30-789513166, I ran FastQC for initial quality checks…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

FastQ QC and Trimming - E5 Coral RNA-seq Data for A.pulchra P.evermanni and P.meandrina Using FastQC fastp and MultiQC on Mox

mox

FastQC

fastp

MultiQC

coral

Acropora pulchra

Porites evermanni

Pocillopora meandrina

2023

After downloading RNA-seq data on 20230516 and then reorganizing the E5 coral RNA-seq data from Azenta project 30-789513166, I ran FastQC for initial quality checks…

<<<<<<< HEAD

Downloaded the E5 coral sRNA-seq data from Azenta project 30-852430235 on 20230515 and the E5 coral RNA-seq data from Azenta project 30-789513166 on 20230516. The data…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Management - E5 Coral RNA-seq and sRNA-seq Reorganizing and Renaming

coral

RNAseq

sRNAseq

2023

Data Management

May 17, 2023

Downloaded the E5 coral sRNA-seq data from Azenta project 30-852430235 on 20230515 and the E5 coral RNA-seq data from Azenta project 30-789513166 on 20230516. The data…

<<<<<<< HEAD

May 17, 2023

Small RNA-seq (sRNA-seq) data was made available from the coral E5 Azenta project 30-789513166. Sample sheet:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Received - Coral RNA-seq Data from Azenta Project 30-789513166

30-789513166

RNA-seq

Azenta

coral

Putnam

2023

Data Received

May 16, 2023

Small RNA-seq (sRNA-seq) data was made available from the coral E5 Azenta project 30-789513166. Sample sheet:

<<<<<<< HEAD

May 16, 2023

Small RNA-seq (sRNA-seq) data was made available from the coral E5 Azenta project 30-852430235. Sample sheet is below.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Received - Coral sRNA-seq Data from Azenta Project 30-852430235

2023

Data Received

May 15, 2023

Small RNA-seq (sRNA-seq) data was made available from the coral E5 Azenta project 30-852430235. Sample sheet is below.

<<<<<<< HEAD

May 15, 2023

After identifying lncRNA in P.generosa, Steven asked that I generate an tissue-specific expression/count matrix (GitHub Issue). Looking through the documentation for StringTie…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

lncRNA Expression - P.generosa lncRNA Expression Using StringTie

2023

Miscellaneous

May 4, 2023

After identifying lncRNA in P.generosa, Steven asked that I generate an tissue-specific expression/count matrix (GitHub Issue). Looking through the documentation for StringTie…

<<<<<<< HEAD

May 4, 2023

After trimming P.generosa RNA-seq reads on 20230426 and then aligning and annotating them to the Panopea-generosa-v1.0 genome on 20230426, I proceeded with the final step of…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Daily Bits - May 2023

2023

Daily Bits

<<<<<<< HEAD

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

lncRNA Identification - P.generosa lncRNAs using CPC2 and bedtools

lncRNA

Panopea generosa

Pacific geoduck

CPC2

bedtools

2023

May 2, 2023

After trimming P.generosa RNA-seq reads on 20230426 and then aligning and annotating them to the Panopea-generosa-v1.0 genome on 20230426, I proceeded with the final step of…

<<<<<<< HEAD

May 2, 2023

At some point, our HPC nodes on Mox will be retired. When that happens, we’ll likely purchase new nodes on the newest UW cluster, Klone. Additionally, the coenv nodes are no…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Containers - Apptainer Explorations

apptainer

singularity

klone

mox

2023

Apr 28, 2023

At some point, our HPC nodes on Mox will be retired. When that happens, we’ll likely purchase new nodes on the newest UW cluster, Klone. Additionally, the coenv nodes are no…

<<<<<<< HEAD

Apr 28, 2023

This is a continuation of the process for identification of lncRNAs,. I aligned FastQs which were previously trimmed earlier today to our Panopea-generosa-v1.0 genome FastA…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcript Alignments - P.generosa RNA-seq Alignments for lncRNA Identification Using Hisat2 StingTie and gffcompare on Mox

gffcompare

mox

Panopea generosa

Pacific geoduck

lncRNA

StringTie

Hisat2

2023

Miscellaneous

This is a continuation of the process for identification of lncRNAs,. I aligned FastQs which were previously trimmed earlier today to our Panopea-generosa-v1.0 genome FastA…

<<<<<<< HEAD

Addressing the update to this GitHub Issue regarding identifying Panopea generosa (Pacific geoduck) long non-coding RNAs (lncRNAs), I used the RNA-seq data from the Nextflow…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

FastQ Trimming and QC - P.generosa RNA-seq Data from 20220323 on Mox

2023

Miscellaneous

Addressing the update to this GitHub Issue regarding identifying Panopea generosa (Pacific geoduck) long non-coding RNAs (lncRNAs), I used the RNA-seq data from the Nextflow…

<<<<<<< HEAD

As part of the CEABIGR project (GitHub repo), Steven asked that I generate an exon expression table (GitHub Issue) where each row is a gene and the columns are the…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Wrangling - CEABIGR C.virginica Exon Expression Table

2023

CEABIGR

Apr 5, 2023

As part of the CEABIGR project (GitHub repo), Steven asked that I generate an exon expression table (GitHub Issue) where each row is a gene and the columns are the…

<<<<<<< HEAD

Apr 5, 2023

Steven tasked me with updating our P.generosa genome annotation file (GitHub Issue) a while back and I finally managed to get it all figured out. Although I wanted to…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Daily Bits - April 2023

2023

Daily Bits

<<<<<<< HEAD

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Wrangling - Append Gene Ontology Aspect to P.generosa Primary Annotation File

2023

Miscellaneous

Mar 29, 2023

Steven tasked me with updating our P.generosa genome annotation file (GitHub Issue) a while back and I finally managed to get it all figured out. Although I wanted to…

<<<<<<< HEAD

Mar 29, 2023

Running DIAMOND BLASTx, followed by MEGAN6 daa-meganizer for taxonomic classification of NOAA M.magister trimmed RNA-seq reads (provided by Giles Goetz on 20230301). This is…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Sequencing Read Taxonomic Classification - M.magister RNA-seq Using DIAMOND BLASTx and MEGAN6 daa-meganizer on Mox

2023

Miscellaneous

Mar 16, 2023

Running DIAMOND BLASTx, followed by MEGAN6 daa-meganizer for taxonomic classification of NOAA M.magister trimmed RNA-seq reads (provided by Giles Goetz on 20230301). This is…

<<<<<<< HEAD

Mar 16, 2023

Transferred trimmed C.magister RNA-seq data from Google Drive to our HPC (Mox) using rclone. This was a great suggestion from Giles Goetz!

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Daily Bits - March 2023

2023

Daily Bits

<<<<<<< HEAD

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Received - Trimmed M.magister RNA-seq from NOAA

2023

Data Received

Mar 1, 2023

Transferred trimmed C.magister RNA-seq data from Google Drive to our HPC (Mox) using rclone. This was a great suggestion from Giles Goetz!

<<<<<<< HEAD

Mar 1, 2023

After some discussion with Steven at Science Hour last week regarding the handling of endosymbiont sequences in the E5 P.verrucosa RNA-seq data, Steven thought it would be…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Sequencing Read Taxonomic Classification - P.verrucosa E5 RNA-seq Using DIAMOND BLASTx and MEGAN daa-meganizer on Mox

2023

Feb 21, 2023

After some discussion with Steven at Science Hour last week regarding the handling of endosymbiont sequences in the E5 P.verrucosa RNA-seq data, Steven thought it would be…

<<<<<<< HEAD

Feb 21, 2023

As part of getting these three coral species genome files (GitHub Issue) added to our Lab Handbook Genomic Resources page, I also need to get the coral endosymbiont…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Wrangling - C.goreaui Genome GFF to GTF Using gffread

2023

Feb 17, 2023

As part of getting these three coral species genome files (GitHub Issue) added to our Lab Handbook Genomic Resources page, I also need to get the coral endosymbiont…

<<<<<<< HEAD

Feb 17, 2023

After getting the RNA-seq data trimmed, it was time to perform alignments and determine expression levels of transcripts/isoforms using with HISAT2 and StringTie…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcript Identification and Alignments - P.verrucosa RNA-seq with Pver_genome_assembly_v1.0 Using HiSat2 and Stringtie on Mox

2023

Feb 16, 2023

After getting the RNA-seq data trimmed, it was time to perform alignments and determine expression levels of transcripts/isoforms using with HISAT2 and StringTie…

<<<<<<< HEAD

Feb 16, 2023

After receiving the P.verrucosa RNA-seq data from Danielle Becker (Hollie Putnam’s Lab, Univ. of Rhode Island), I noticed that the trimmed reads didn’t appear to actually be…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

FastQ Trimming and QC - P.verrucosa RNA-seq Data from Danielle Becker in Hollie Putnam Lab Using fastp FastQC and MultiQC on Mox

2023

After receiving the P.verrucosa RNA-seq data from Danielle Becker (Hollie Putnam’s Lab, Univ. of Rhode Island), I noticed that the trimmed reads didn’t appear to actually be…

<<<<<<< HEAD

Steven asked that I create a karyotype file (GitHub Issue) from the NCBI P.verrucosa genome (GCA_014529365.1) in the following format:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Wrangling - Create P.verrucosa GCA_014529365.1 Karyotype File

2023

Steven asked that I create a karyotype file (GitHub Issue) from the NCBI P.verrucosa genome (GCA_014529365.1) in the following format:

<<<<<<< HEAD

Worked with Danielle Becker, as part of the Coral E5 project, to transfer data related to her repo, from her HPC (Univ. of Rhode Island; Andromeda) to ours (Univ. of…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Received - P.verrucosa RNA-seq and WGBS Full Data from Danielle Becker

2023

Data Received

Feb 10, 2023

Worked with Danielle Becker, as part of the Coral E5 project, to transfer data related to her repo, from her HPC (Univ. of Rhode Island; Andromeda) to ours (Univ. of…

<<<<<<< HEAD

Feb 10, 2023

Working on this Issue regarding adding coral genomes to our Handbook (GitHub) and needed to generate a HISAT2 index to add to The Roberts Lab Handbook Genomic Resources.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Daily Bits - February 2023

2023

Daily Bits

<<<<<<< HEAD

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genome Indexing - P.verrucosa v1.0 Assembly with HiSat2 on Mox

2023

Miscellaneous

Working on this Issue regarding adding coral genomes to our Handbook (GitHub) and needed to generate a HISAT2 index to add to The Roberts Lab Handbook Genomic Resources.

<<<<<<< HEAD

Working on this Issue regarding adding coral genomes to our Handbook (GitHub) and needed to generate a HISAT2 index to add to The Roberts Lab Handbook Genomic Resources.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genome Indexing - M.capitata HIv3 Assembly with HiSat2 on Mox

2023

Miscellaneous

Working on this Issue regarding adding coral genomes to our Handbook (GitHub) and needed to generate a HISAT2 index to add to The Roberts Lab Handbook Genomic Resources.

<<<<<<< HEAD

Working on this Issue regarding adding coral genomes to our Handbook (GitHub) and needed to generate a HISAT2 index to add to The Roberts Lab Handbook Genomic Resources.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genome Indexing - P.acuta HIv2 Assembly with HiSat2 on Mox

Poccillopora acuta

coral

HIv2

hisat2

mox

index

2023

Working on this Issue regarding adding coral genomes to our Handbook (GitHub) and needed to generate a HISAT2 index to add to The Roberts Lab Handbook Genomic Resources.

<<<<<<< HEAD

As part of getting these three coral species genome files (GitHub Issue) added to our Lab Handbook Genomic Resources page, I will index the P.verrucosa genome file (Pver_geno…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Wrangling - P.verrucosa Genome GFF to GTF Using gffread

2023

Miscellaneous

As part of getting these three coral species genome files (GitHub Issue) added to our Lab Handbook Genomic Resources page, I will index the P.verrucosa genome file (Pver_geno…

<<<<<<< HEAD

As part of getting these three coral species genome files (GitHub Issue) added to our Lab Handbook Genomic Resources page, I will index the M.capitata genome file (Montipora_…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Wrangling - M.capitata Genome GFF to GTF Using gffread

2023

Miscellaneous

As part of getting these three coral species genome files (GitHub Issue) added to our Lab Handbook Genomic Resources page, I will index the M.capitata genome file (Montipora_…

<<<<<<< HEAD

As part of getting these three coral species genome files (GitHub Issue) added to our Lab Handbook Genomic Resources page, I will index the P.acuta genome file using HISAT2…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Wrangling - P.acuta Genome GFF to GTF Conversion Using gffread

2023

Miscellaneous

Jan 26, 2023

As part of getting these three coral species genome files (GitHub Issue) added to our Lab Handbook Genomic Resources page, I will index the P.acuta genome file using HISAT2…

<<<<<<< HEAD

Jan 26, 2023

Working on this Issue regarding adding coral genomes to our Handbook (GitHub) and needed to generate a HISAT2 index to add to The Roberts Lab Handbook Genomic Resources.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genome Indexing - P.verrucosa NCBI GCA_014529365.1 with HiSat2 on Mox

2023

Miscellaneous

Working on this Issue regarding adding coral genomes to our Handbook (GitHub) and needed to generate a HISAT2 index to add to The Roberts Lab Handbook Genomic Resources.

<<<<<<< HEAD

Working on this Issue regarding adding coral genomes to our Handbook (GitHub) and needed to generate a HISAT2 index to add to The Roberts Lab Handbook Genomic Resources.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genome Indexing - M.capitata NCBI GCA_006542545.1 with HiSat2 on Mox

hisat2

Montipora capitata

coral

GCA_006542545.1

mox

2023

Miscellaneous

Working on this Issue regarding adding coral genomes to our Handbook (GitHub) and needed to generate a HISAT2 index to add to The Roberts Lab Handbook Genomic Resources.

<<<<<<< HEAD

Per this GitHub Issue, Steven wanted me to download all of the SRA data (RNA-seq and WGBS-seq) from NCBI BioProject PRJNA744403 and run QC on the data.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

SRA Data - Coral SRA BioProject PRJNA744403 Download and QC

PRJNA744403

SRA

NCBI

fastp

FastQC

MultiQC

coral

metagenomics

2023

Miscellaneous

Jan 13, 2023

Per this GitHub Issue, Steven wanted me to download all of the SRA data (RNA-seq and WGBS-seq) from NCBI BioProject PRJNA744403 and run QC on the data.

<<<<<<< HEAD

Jan 13, 2023

Plot CEABIGR coefficients of variation comparisons of mean gene methylation.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Monthly Goals - January 2023

2023

Monthly Goals

Jan 5, 2023

Plot CEABIGR coefficients of variation comparisons of mean gene methylation.

<<<<<<< HEAD

Jan 5, 2023

Yaamini asked me to run the epidiverse/snp pipeline (GitHub Issue) on her Haws Crassostrea gigas (Pacific oyster) Hawaii bisuflite sequencing BAMs for SNP identification.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Daily Bits - January 2023

2023

Daily Bits

<<<<<<< HEAD

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

BS-Seq Analysis - Nextflow EpiDiverse SNP Pipeline for Haws Hawaii C.gigas BAMs from Yaamini Base Config

2022

Miscellaneous

Dec 15, 2022

Yaamini asked me to run the epidiverse/snp pipeline (GitHub Issue) on her Haws Crassostrea gigas (Pacific oyster) Hawaii bisuflite sequencing BAMs for SNP identification.

<<<<<<< HEAD

Dec 15, 2022

Yaamini asked me to run the epidiverse/snp pipeline (GitHub Issue) on her Haws Crassostrea gigas (Pacific oyster) Hawaii bisuflite sequencing BAMs for SNP identification.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

BS-Seq Analysis - Nextflow EpiDiverse SNP Pipeline for Haws Hawaii C.gigas BAMs from Yaamini

2022

Miscellaneous

Dec 14, 2022

Yaamini asked me to run the epidiverse/snp pipeline (GitHub Issue) on her Haws Crassostrea gigas (Pacific oyster) Hawaii bisuflite sequencing BAMs for SNP identification.

<<<<<<< HEAD

Dec 14, 2022

Working on the CEABIGR project, I was preparing to make a gene expression file to use in CIRCOS (GitHub Issue) when I realized that the Ballgown gene expression file (CSV;…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Daily Bits - December 2022

2022

Daily Bits

<<<<<<< HEAD

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Daily Bits - November 2022

2022

Daily Bits

<<<<<<< HEAD

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Daily Bits - October 2022

2022

Daily Bits

<<<<<<< HEAD

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Wrangling - C.virginica NCBI GCF_002022765.2 GFF to Gene and Pseudogene Combined BED File

2022

Miscellaneous

Sep 26, 2022

Working on the CEABIGR project, I was preparing to make a gene expression file to use in CIRCOS (GitHub Issue) when I realized that the Ballgown gene expression file (CSV;…

<<<<<<< HEAD

Sep 26, 2022

Steven asked that I identify SNPs from our C.virginica CEABIGR BSseq data (GitHub Issue). So, I ran sorted, deduplicated Bismark BAMs that Steven generated through the EpiDiv…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

BSseq SNP Analysis - Nextflow EpiDiverse SNP Pipeline for C.virginica CEABIGR BSseq data

2022

Miscellaneous

Sep 21, 2022

Steven asked that I identify SNPs from our C.virginica CEABIGR BSseq data (GitHub Issue). So, I ran sorted, deduplicated Bismark BAMs that Steven generated through the EpiDiv…

<<<<<<< HEAD

Sep 21, 2022

During today’s discussion, Yaamini recommended we generate a list of genes with different predominant isoforms between females and males, while also adding a column with a…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Wrangling - Identify C.virginica Genes with Different Predominant Isoforms for CEABIGR

2022

CEABIGR

Sep 20, 2022

During today’s discussion, Yaamini recommended we generate a list of genes with different predominant isoforms between females and males, while also adding a column with a…

<<<<<<< HEAD

Sep 20, 2022

As part of identifying long non-coding RNA (lncRNA) in Pacific geoduck(GitHub Issue), one of the first things that I wanted to do was to gather all of our geoduck RNAseq…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNAseq Alignments - P.generosa Alignments and Alternative Transcript Identification Using Hisat2 and StringTie on Mox

2022

Miscellaneous

Sep 14, 2022

As part of identifying long non-coding RNA (lncRNA) in Pacific geoduck(GitHub Issue), one of the first things that I wanted to do was to gather all of our geoduck RNAseq…

<<<<<<< HEAD

Sep 14, 2022

Per this GitHub Issue, Steven asked me to identify long non-coding RNA (lncRNA) in geoduck. The first step is to aggregate all of our Panopea generosa (Pacific geoduck) RNAse…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

FastQ Trimming - Geoduck RNAseq Data Using fastp on Mox

2022

Miscellaneous

Sep 8, 2022

Per this GitHub Issue, Steven asked me to identify long non-coding RNA (lncRNA) in geoduck. The first step is to aggregate all of our Panopea generosa (Pacific geoduck) RNAse…

<<<<<<< HEAD

Sep 8, 2022

The trimmming described below is probably incomplete and should be ignored.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Daily Bits - September 2022

September

2022

Daily Bits

<<<<<<< HEAD

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

FastQ Trimming and QC - C.virginica Larval BS-seq Data from Lotterhos Lab and Part of CEABIGR Project Using fastp on Mox

BSseq

Lotterhos

CEABIGR

Crassostrea virginica

Eastern oyster

fastp

mox

2022

Miscellaneous

Aug 29, 2022

The trimmming described below is probably incomplete and should be ignored.

<<<<<<< HEAD

Aug 29, 2022

In preparation for isoform identificaiton/quantification in S.namaycush RNAseq data, Ballgown will need a genes-only BED file. To generate, I used GFFutils to extract only…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Wrangling - Convert S.namaycush NCBI GFF to genes-only BED file for Use in Ballgown Analysis

2022

Miscellaneous

Aug 18, 2022

In preparation for isoform identificaiton/quantification in S.namaycush RNAseq data, Ballgown will need a genes-only BED file. To generate, I used GFFutils to extract only…

<<<<<<< HEAD

Aug 18, 2022

After previously downloading/trimming/QCing S.namaycush SRA liver RNAseq data on 20220706, Steven asked that I run through Hisat2 for splice site identification (GitHub…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Splice Site Identification - S.namaycush Liver Parasitized and Non-Parasitized SRA RNAseq Using Hisat2-Stingtie with Genome GCF_016432855.1

2022

Miscellaneous

Aug 10, 2022

After previously downloading/trimming/QCing S.namaycush SRA liver RNAseq data on 20220706, Steven asked that I run through Hisat2 for splice site identification (GitHub…

<<<<<<< HEAD

Aug 10, 2022

My previous qPCR on these cDNA using ferritin primers (SRIDs: 1808, 1809) resulted in no amplification. This was a bit surprising and makes me suspect that I screwed up…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Repeat of Mussel Gill Heat Stress cDNA with Ferritin Primers

2022

Miscellaneous

Aug 4, 2022

My previous qPCR on these cDNA using ferritin primers (SRIDs: 1808, 1809) resulted in no amplification. This was a bit surprising and makes me suspect that I screwed up…

<<<<<<< HEAD

Aug 4, 2022

Ran qPCRs on Dorothy’s mussel gill cDNA from 20220726 using the following primers:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Daily Bits - August 2022

August

2022

Daily Bits

<<<<<<< HEAD

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Dorothys Mussel cDNA from 20220726

2022

Miscellaneous

Jul 27, 2022

Ran qPCRs on Dorothy’s mussel gill cDNA from 20220726 using the following primers:

<<<<<<< HEAD

Jul 27, 2022

Isolated RNA from a subset of Dorothy’s mussel gill samples:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation and Quantification - Dorothy Mussel Gill Samples

2022

Miscellaneous

Jul 26, 2022

Isolated RNA from a subset of Dorothy’s mussel gill samples:

<<<<<<< HEAD

Jul 26, 2022

Alrighty, this notebook entry is going to have a lot to unpack, as the process to get these pipelines running and then deal with the actual data we wanted to run them with…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

BS-seq and SNP Analysis - Nextflow EpiDiverse Pipelines Trials and Tribulations

2022

Miscellaneous

Jul 25, 2022

Alrighty, this notebook entry is going to have a lot to unpack, as the process to get these pipelines running and then deal with the actual data we wanted to run them with…

<<<<<<< HEAD

Jul 25, 2022

Per this GitHub Issue, which I accidentally forgot about for three weeks (!), Steven wanted me to download the lake trout (Salvelinus namaycush) RNAseq data from NCBI…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

SRA Data - S.namaycush SRA BioProject PRJNA674328 Download and QC

2022

Miscellaneous

Jul 6, 2022

Per this GitHub Issue, which I accidentally forgot about for three weeks (!), Steven wanted me to download the lake trout (Salvelinus namaycush) RNAseq data from NCBI…

<<<<<<< HEAD

Jul 6, 2022

Submitted our Ostrea lurida (Olympia oyster) MBD BS-seq data from 20160203 to the NCBI Sequence Read Archive (SRA).

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Daily Bits - July 2022

2022

Daily Bits

<<<<<<< HEAD

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Daily Bits - June 2022

2022

Daily Bits

<<<<<<< HEAD

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

SRA Submission - Ostrea lurida MBD BS-seq from 20160203

2022

SRA Submission

Jun 15, 2022

Submitted our Ostrea lurida (Olympia oyster) MBD BS-seq data from 20160203 to the NCBI Sequence Read Archive (SRA).

<<<<<<< HEAD

Jun 15, 2022

This will be a “dynamic” notebook entry, whereby I will update this post continually as I process new samples, analyze new data, etc for this project. The hope is to make it…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Project Summary - C.virginica CEABiGR - Female vs. Male Gonad Exposed to OA

Crassostrea virginica

CEABIGR

gonad

Eastern oyster

2022

Project Summary

Apr 25, 2022

This will be a “dynamic” notebook entry, whereby I will update this post continually as I process new samples, analyze new data, etc for this project. The hope is to make it…

<<<<<<< HEAD

Apr 25, 2022

Steven asked me to create a canonical genome annotation file (GitHub Issue). I needed/wanted to create a file containing gene IDs, SwissProt (SP) IDs, gene names, gene…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Wrangling - Create Primary P.generosa Genome Annotation File

2022

Miscellaneous

Apr 19, 2022

Steven asked me to create a canonical genome annotation file (GitHub Issue). I needed/wanted to create a file containing gene IDs, SwissProt (SP) IDs, gene names, gene…

<<<<<<< HEAD

Apr 19, 2022

Steven asked that I isolate RNA from the remainder of the Berdahl brain tissue samples (GitHub issue).

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation - O.nerka Berdahl Brain Tissues

2022

Miscellaneous

Apr 11, 2022

Steven asked that I isolate RNA from the remainder of the Berdahl brain tissue samples (GitHub issue).

<<<<<<< HEAD

Apr 11, 2022

We had been encountering issues when linking to images in GitHub (e.g. notebooks, Issues/Discussions) hosted on our servers (primarily Gannet). Images always showed up as…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Server Maintenance - Fix Server Certificate Authentication Issues

github

InCommon

certificate

servers

gannet

owl

eagle

2022

Computer Servicing

Apr 2, 2022

We had been encountering issues when linking to images in GitHub (e.g. notebooks, Issues/Discussions) hosted on our servers (primarily Gannet). Images always showed up as…

<<<<<<< HEAD

Apr 2, 2022

For some reason, I struggled to get things installed correctly. Installing Nextflow was straightforward and didn’t have any issues. First bump in the road came from the insta…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Nextflow - Trials and Tribulations of Installing and Using NF-Core RNAseq

2022

Miscellaneous

Mar 25, 2022

For some reason, I struggled to get things installed correctly. Installing Nextflow was straightforward and didn’t have any issues. First bump in the road came from the insta…

<<<<<<< HEAD

Mar 25, 2022

Steven wanted me to generate FastA files (GitHub Issue) for Panopea generosa (Pacific geoduck) coding sequences (CDS), genes, and mRNAs. One of the primary needs, though…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Wrangling - P.generosa Genomic Feature FastA Creation

2022

Miscellaneous

Mar 24, 2022

Steven wanted me to generate FastA files (GitHub Issue) for Panopea generosa (Pacific geoduck) coding sequences (CDS), genes, and mRNAs. One of the primary needs, though…

<<<<<<< HEAD

Mar 24, 2022

Steven asked that I obtain relative expression values for various geoduck tissues (GitHub Issue). So, I decided to use this as an opportunity to try to use a Nextflow pipelin…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Differential Gene Expression - P.generosa DGE Between Tissues Using Nextlow NF-Core RNAseq Pipeline on Mox

nextflow

Panopea generosa

Pacific geoduck

RNAseq

nf-core

mox

2022

Miscellaneous

Mar 23, 2022

Steven asked that I obtain relative expression values for various geoduck tissues (GitHub Issue). So, I decided to use this as an opportunity to try to use a Nextflow pipelin…

<<<<<<< HEAD

Mar 23, 2022

After performing DIAMOND BLASTx and DAA “meganization” on 20220302, the next step was to import the DAA files into MEGAN6 for analyzing the resulting taxonomic assignments…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Analysis - C.virginica BSseq Unmapped Reads Using MEGAN6

2022

Miscellaneous

Mar 9, 2022

After performing DIAMOND BLASTx and DAA “meganization” on 20220302, the next step was to import the DAA files into MEGAN6 for analyzing the resulting taxonomic assignments…

<<<<<<< HEAD

Mar 9, 2022

After realizing that the Crassostrea virginica (Eastern oyster) RNAseq data had relatively low alignment rates (see this notebook entry from 20220224 for a bit more…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Analysis - C.virginica RNAseq Zymo ZR4059 Analyzed by ZymoResearch

2022

Miscellaneous

After realizing that the Crassostrea virginica (Eastern oyster) RNAseq data had relatively low alignment rates (see this notebook entry from 20220224 for a bit more…

<<<<<<< HEAD

After mapping bisulfite sequencing (BSseq) data to the Crassostrea virginica (Eastern oyster) genome, Steven noticed that there were a large number of unmapped reads. He…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Taxonomic Assignment - C.virginica BSseq Unmapped Reads Using DIAMOND BLASTx and MEGAN6 on Mox

2022

Miscellaneous

After mapping bisulfite sequencing (BSseq) data to the Crassostrea virginica (Eastern oyster) genome, Steven noticed that there were a large number of unmapped reads. He…

<<<<<<< HEAD

Steven asked in this GitHub Issue to convert our Panopea generosa (Pacific geoduck) genomic GFF to a GTF for use in the 10x Genomics Cell Ranger software. This conversion…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Wrangling - P.generosa Genome GFF Conversion to GTF Using gffread

2022

Miscellaneous

Mar 1, 2022

Steven asked in this GitHub Issue to convert our Panopea generosa (Pacific geoduck) genomic GFF to a GTF for use in the 10x Genomics Cell Ranger software. This conversion…

<<<<<<< HEAD

Mar 1, 2022

After an additional round of trimming yesterday, I needed to identify alternative transcripts in the Crassostrea virginica (Eastern oyster) gonad RNAseq data we have. I…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcript Identification and Alignments - C.virginica RNAseq with NCBI Genome GCF_002022765.2 Using Hisat2 and Stringtie on Mox

hisat2

stringtie

Crassostrea virginica

Eastern oyster

RNAseq

GCF_002022765.2

2022

Miscellaneous

Feb 25, 2022

After an additional round of trimming yesterday, I needed to identify alternative transcripts in the Crassostrea virginica (Eastern oyster) gonad RNAseq data we have. I…

<<<<<<< HEAD

Feb 25, 2022

When I previously aligned trimmed RNAseq reads to the NCBI C.virginica genome (GCF_002022765.2) on 20210726, I specifically noted that alignment rates were consistently…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Trimming - Additional 20bp from C.virginica Gonad RNAseq with fastp on Mox

fastp

mox

Crassostrea virginica

RNAseq

trimming

Eastern oyster

2022

Miscellaneous

Feb 24, 2022

When I previously aligned trimmed RNAseq reads to the NCBI C.virginica genome (GCF_002022765.2) on 20210726, I specifically noted that alignment rates were consistently…

<<<<<<< HEAD

Feb 24, 2022

Continuing to work on our Crassostrea virginica (Eastern oyster) project examining the effects of OA on female and male gonads (GitHub repo), Steven tasked me with parsing…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Wrangling - C.virginica lncRNA Extractions from NCBI GCF_002022765.2 Using GffRead

2022

Miscellaneous

Feb 17, 2022

Continuing to work on our Crassostrea virginica (Eastern oyster) project examining the effects of OA on female and male gonads (GitHub repo), Steven tasked me with parsing…

<<<<<<< HEAD

Feb 17, 2022

As part of this project, Steven’s asked that I identify long, non-coding RNAs (lncRNAs) (GitHub Issue) in the Crassostrea virginica (Eastern oyster) adult OA gonad RNAseq…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Assembly - Genome-guided C.virginica Adult Gonad OA RNAseq Using Trinity on Mox

2022

Miscellaneous

Feb 7, 2022

As part of this project, Steven’s asked that I identify long, non-coding RNAs (lncRNAs) (GitHub Issue) in the Crassostrea virginica (Eastern oyster) adult OA gonad RNAseq…

<<<<<<< HEAD

Feb 7, 2022

As part of this project epigeneticstoocean/2018_L18-adult-methylation (private GitHub repo), Steven’s asked that I identify long, non-coding RNAs (lncRNAs) (GitHub Issue) in…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNAseq Alignment - C.virginica Adult OA Gonad Data to GCF_002022765.2 Genome Using HISAT2 on Mox

HISAT2

Crassostrea virginica

RNAseq

Mox

Eastern oyster

2022

Miscellaneous

Jan 31, 2022

As part of this project epigeneticstoocean/2018_L18-adult-methylation (private GitHub repo), Steven’s asked that I identify long, non-coding RNAs (lncRNAs) (GitHub Issue) in…

<<<<<<< HEAD

Jan 31, 2022

As we continue to work on the analysis of impacts of OA on Crassostrea virginica (Eastern oyster) gonads via DNA methylation and RNAseq…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Wrangling - C.virginica Gonad RNAseq Transcript Counts Per Gene Per Sample Using Ballgown

data wrangling

Crassostrea virginica

eastern oyster

ballgown

2022

Miscellaneous

Jan 27, 2022

As we continue to work on the analysis of impacts of OA on Crassostrea virginica (Eastern oyster) gonads via DNA methylation and RNAseq…

<<<<<<< HEAD

Jan 27, 2022

In this GitHub Issue Steven asked that I download Crassostrea virginica (Eastern oyster) OA larval DNA methylation sequencing data from the Lotterhos Lab. The data is part…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Received - C.virginica OA Larvae DNA Methylation FastQs from Lotterhos Lab

Crassostrea virginica

Eastern oyster

larvae

DNA methylation

data received

2022

Data Received

Jan 19, 2022

In this GitHub Issue Steven asked that I download Crassostrea virginica (Eastern oyster) OA larval DNA methylation sequencing data from the Lotterhos Lab. The data is part…

<<<<<<< HEAD

Jan 19, 2022

This will be a “dynamic” notebook entry, whereby I will update this post continually as I process new samples, analyze new data, etc for this project. The hope is to make it…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Project Summary - Matt George PSMFC Mytilus Byssus Project

2022

Project Summary

Jan 13, 2022

This will be a “dynamic” notebook entry, whereby I will update this post continually as I process new samples, analyze new data, etc for this project. The hope is to make it…

<<<<<<< HEAD

Jan 13, 2022

The previous round of RNA isolation on 20211222 had poor yields for the brain tissue. As such, I needed to attempt to obtain RNA from some additional brain tissues.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation - O.nerka Berdahl Brain Tissues

2022

Miscellaneous

The previous round of RNA isolation on 20211222 had poor yields for the brain tissue. As such, I needed to attempt to obtain RNA from some additional brain tissues.

<<<<<<< HEAD

As part of a mussel project that Matt George has with the Pacific States Marine Fisheries Commission (PSMFC), I’m helping by continuing isolating RNA from a relatively large…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation - M.trossulus Gill

2022

Miscellaneous

As part of a mussel project that Matt George has with the Pacific States Marine Fisheries Commission (PSMFC), I’m helping by continuing isolating RNA from a relatively large…

<<<<<<< HEAD

As part of a mussel project that Matt George has with the Pacific States Marine Fisheries Commission (PSMFC), I’m helping by continuing isolating RNA from a relatively large…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation - M.trossulus Gill and Phenol Gland

2022

Miscellaneous

Jan 11, 2022

As part of a mussel project that Matt George has with the Pacific States Marine Fisheries Commission (PSMFC), I’m helping by continuing isolating RNA from a relatively large…

<<<<<<< HEAD

Jan 11, 2022

As part of a mussel project that Matt George has with the Pacific States Marine Fisheries Commission (PSMFC), I’m helping by continuing isolating RNA from a relatively large…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation - M.trossulus Gill and Phenol Gland

2022

Miscellaneous

Jan 10, 2022

As part of a mussel project that Matt George has with the Pacific States Marine Fisheries Commission (PSMFC), I’m helping by continuing isolating RNA from a relatively large…

<<<<<<< HEAD

Jan 10, 2022

As part of a mussel project that Matt George has with the Pacific States Marine Fisheries Commission (PSMFC), I’m helping by continuing isolating RNA from a relatively large…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation - M.trossulus Gill and Phenol Gland

2022

Miscellaneous

Jan 9, 2022

As part of a mussel project that Matt George has with the Pacific States Marine Fisheries Commission (PSMFC), I’m helping by continuing isolating RNA from a relatively large…

<<<<<<< HEAD

Jan 9, 2022

As part of a mussel project that Matt George has with the Pacific States Marine Fisheries Commission (PSMFC), I’m helping by continuing isolating RNA from a relatively large…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation - M.trossulus Phenol Gland and Gill

2021

Miscellaneous

Dec 23, 2021

As part of a mussel project that Matt George has with the Pacific States Marine Fisheries Commission (PSMFC), I’m helping by continuing isolating RNA from a relatively large…

<<<<<<< HEAD

Dec 23, 2021

As part of a mussel project that Matt George has with the Pacific States Marine Fisheries Commission (PSMFC), I’m helping by isolating RNA from a relatively large number of…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation - M.trossulus Foot and Phenol Gland

2021

Miscellaneous

As part of a mussel project that Matt George has with the Pacific States Marine Fisheries Commission (PSMFC), I’m helping by isolating RNA from a relatively large number of…

<<<<<<< HEAD

This will be a “dynamic” notebook entry, whereby I will update this post continually as I process new samples, analyze new data, etc for this project. The hope is to make it…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Project Summary - O.nerka Berdahl Samples

2021

Project Summary

This will be a “dynamic” notebook entry, whereby I will update this post continually as I process new samples, analyze new data, etc for this project. The hope is to make it…

<<<<<<< HEAD

The previous round of RNA isolation (on 20211220) had poor yields for the brain tissue. As such, I needed to attempt to obtain RNA from some additional brain tissues.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation - O.nerka Berdahl Brain Tissues

2021

Miscellaneous

The previous round of RNA isolation (on 20211220) had poor yields for the brain tissue. As such, I needed to attempt to obtain RNA from some additional brain tissues.

<<<<<<< HEAD

Finally got around to tackling this GitHub issue regarding isolating RNA from some Oncorhynchus nerka (sockeye salmon) tissues we have from Andrew Berdahl’s lab (a UW SAFS…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation - O.nerka Berdahl Tissues

RNA isolation

qubit

RNA quantification

RNA

2021

Miscellaneous

Dec 20, 2021

Finally got around to tackling this GitHub issue regarding isolating RNA from some Oncorhynchus nerka (sockeye salmon) tissues we have from Andrew Berdahl’s lab (a UW SAFS…

<<<<<<< HEAD

Dec 20, 2021

When working to identify differentially expressed transcripts (DETs) and genes (DEGs) for our Crassostrea virginica (Eastern oyster) RNAseq/DNA methylation comparison of…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Wrangling - C.virginica NCBI GCF_002022765.2 GFF to Gene BED File

2021

Miscellaneous

Dec 9, 2021

When working to identify differentially expressed transcripts (DETs) and genes (DEGs) for our Crassostrea virginica (Eastern oyster) RNAseq/DNA methylation comparison of…

<<<<<<< HEAD

Dec 9, 2021

In preparation for differential transcript analysis, I previously ran our RNAseq data through StringTie on 20210726 to identify and quantify transcripts. Identification of…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Differential Transcript Expression - C.virginica Gonad RNAseq Using Ballgown

Crassostrea virginica

Eastern oyster

gonad

RNAseq

ballgown

DEG

DET

expression

2021

Miscellaneous

Oct 21, 2021

In preparation for differential transcript analysis, I previously ran our RNAseq data through StringTie on 20210726 to identify and quantify transcripts. Identification of…

<<<<<<< HEAD

Oct 21, 2021

I previously identified variants across the four Day 2 DEG pooled RNAseq samples (380822, 380823, 380824, 380825) on 20210909 within the cbai_transcriptome_v3.1 transcriptome…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

SNP Characterization - C.bairdi v3.1 Transcriptome Assembly and Day2 DEG Pooled Samples RNAseq Data

2021

Tanner Crab RNAseq

Oct 5, 2021

I previously identified variants across the four Day 2 DEG pooled RNAseq samples (380822, 380823, 380824, 380825) on 20210909 within the cbai_transcriptome_v3.1 transcriptome…

<<<<<<< HEAD

Oct 5, 2021

After getting our the RNAseq data aligned with HISAT2 on 20210908, the next step was to make variant calls. I opted to do so using bcftools mpileup. Previously, this was…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

SNP Identification - C.bairdi Day 2 DEG Pooled Samples Using bcftools on Mox

bcftools

Tanner crab

Chionoecetes bairdi

Mox

SNP

2021

Tanner Crab RNAseq

Sep 9, 2021

After getting our the RNAseq data aligned with HISAT2 on 20210908, the next step was to make variant calls. I opted to do so using bcftools mpileup. Previously, this was…

<<<<<<< HEAD

Sep 9, 2021

Ealier today, I created the necessary Hisat2 index files for cbai_transcriptome_v3.1. Next, I needed to actually get the alignments run. The alignments were performed using H…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNAseq Alignments - C.bairdi Day 2 Infected-Uninfected Temperature Increase-Decrease RNAseq to cbai_transcriptome_v3.1.fasta with Hisat2 on Mox

hisat2

alignment

RNAseq

Tanner crab

Chionoecetes bairdi

mox

2021

Tanner Crab RNAseq

Ealier today, I created the necessary Hisat2 index files for cbai_transcriptome_v3.1. Next, I needed to actually get the alignments run. The alignments were performed using H…

<<<<<<< HEAD

We recently received reviews back for the Tanner crab paper submission (“Characterization of the gene repertoire and environmentally driven expression patterns in Tanner…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Assembly Indexing - C.bairdi Transcriptome cbai_transcriptome_v3.1.fasta with Hisat2 on Mox

2021

Tanner Crab RNAseq

We recently received reviews back for the Tanner crab paper submission (“Characterization of the gene repertoire and environmentally driven expression patterns in Tanner…

<<<<<<< HEAD

Replaced the battery pack in the top APC SUA2200RM2U UPS in our computing “cluster” cabinet.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Computer Servicing - APC SUA2200RM2U UPS Battery Replacement

battery

ups

apc

2021

Computer Servicing

Replaced the battery pack in the top APC SUA2200RM2U UPS in our computing “cluster” cabinet.

<<<<<<< HEAD

We’ve been having an issue with our computer Raven where it would become inaccessible after some time after a reboot. Attempts to remote in would just indicate no route to…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Computer Management - Disable Sleep and Hibernation on Raven

raven

ubuntu

sleep

2021

Computer Servicing

We’ve been having an issue with our computer Raven where it would become inaccessible after some time after a reboot. Attempts to remote in would just indicate no route to…

<<<<<<< HEAD

Replace battery in uninterruptible power supply APS BR1000G for Owl in FTR 230.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Uninterruptible Power Supply - Battery Replacement for APS BR1000G

2021

Computer Servicing

Aug 11, 2021

Replace battery in uninterruptible power supply APS BR1000G for Owl in FTR 230.

<<<<<<< HEAD

Aug 11, 2021

After having run HISAT2 to index and identify exons and splice sites in the NCBI Crassostrea virginica (Eastern oyster) genome (GCF_002022765.2) on 20210720, the next step…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcript Identification and Quantification - C.virginia RNAseq With NCBI Genome GCF_002022765.2 Using StringTie on Mox

2021

Miscellaneous

Jul 26, 2021

After having run HISAT2 to index and identify exons and splice sites in the NCBI Crassostrea virginica (Eastern oyster) genome (GCF_002022765.2) on 20210720, the next step…

<<<<<<< HEAD

Jul 26, 2021

Previously performed quality trimming on the Crassostrea virginica (Eastern oyster) gonad/sperm RNAseq data on 20210714. Next, I needed to identify exons and splice sites…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genome Annotations - Splice Site and Exon Extractions for C.virginica GCF_002022765.2 Genome Using Hisat2 on Mox

2021

Miscellaneous

Jul 20, 2021

Previously performed quality trimming on the Crassostrea virginica (Eastern oyster) gonad/sperm RNAseq data on 20210714. Next, I needed to identify exons and splice sites…

<<<<<<< HEAD

Jul 20, 2021

Needed to trim the Crassostrea virginica (Eastern oyster) gonad RNAseq data we received on 20210528.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Trimming - C.virginica Gonad RNAseq with FastP on Mox

2021

Miscellaneous

Jul 14, 2021

Needed to trim the Crassostrea virginica (Eastern oyster) gonad RNAseq data we received on 20210528.

<<<<<<< HEAD

Jul 14, 2021

Per this GitHub Issue, I’ve compiled a summary table, with links, of all of our Panopea generosa (Pacific geoduck) RNAseq data as it exists in NCBI. This will be a “dynamic”…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Summary - Geoduck RNAseq Data

2021

Project Summary

Per this GitHub Issue, I’ve compiled a summary table, with links, of all of our Panopea generosa (Pacific geoduck) RNAseq data as it exists in NCBI. This will be a “dynamic”…

<<<<<<< HEAD

As part of our Panopea generosa (Pacific geoduck) genome sequencing efforts, Steven came across a tool designed to help identify if there are any contaminating sequences in…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genome Analysis - Identification of Potential Contaminating Sequences in Panopea-generosa-v1.0 Assembly Using BlobToolKit on Mox

2021

Geoduck Genome Sequencing

As part of our Panopea generosa (Pacific geoduck) genome sequencing efforts, Steven came across a tool designed to help identify if there are any contaminating sequences in…

<<<<<<< HEAD

Finally got around to running FastQC on Yaamini’s RNAseq and WGBS sequencing data recieved on 20210528.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

FastQC-MultiQC - Yaamini’s C.virginica RNAseq and WGBS from ZymoResearch on Mox

2021

Miscellaneous

Jun 29, 2021

Finally got around to running FastQC on Yaamini’s RNAseq and WGBS sequencing data recieved on 20210528.

<<<<<<< HEAD

Jun 29, 2021

Shelly posted a GitHub Issue asking if I could create a file of S.salar genes with their UniProt annotations (e.g. gene name, UniProt accession, GO terms).

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Wrangling - S.salar Gene Annotations from NCBI RefSeq GCF_000233375.1_ICSASG_v2_genomic.gff for Shelly

2021

Miscellaneous

Jun 1, 2021

Shelly posted a GitHub Issue asking if I could create a file of S.salar genes with their UniProt annotations (e.g. gene name, UniProt accession, GO terms).

<<<<<<< HEAD

Jun 1, 2021

Yaamini received her sequencing data from ZymoResearch; both whole genome bisfulfite sequencing (WGBS) and RNAseq. I was tasked with downloading the data and running QC.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Received - Yaamini’s C.virginica WGBS and RNAseq Data from ZymoResearch

2021

Data Received

May 28, 2021

Yaamini received her sequencing data from ZymoResearch; both whole genome bisfulfite sequencing (WGBS) and RNAseq. I was tasked with downloading the data and running QC.

<<<<<<< HEAD

May 28, 2021

After generating a new Ostrea lurida genome assembly (v090) on 20210520, I decided to compare with our previous genome assemblies. Here, I compared v090 with all of our…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Assembly Comparisons - Ostrea lurida Non-scaffold Genome Assembly Comparisons Using Quast on Swoose

swoose

quast

Ostrea lurida

Olympia oyster

2021

Olympia Oyster Genome Assembly

After generating a new Ostrea lurida genome assembly (v090) on 20210520, I decided to compare with our previous genome assemblies. Here, I compared v090 with all of our…

<<<<<<< HEAD

After running a new Ostrea lurida assembly yesterday (Olurida_v090), I evaluated Olurida_v090 using Quast to produce some stats. This was run on my local computer with the…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Assembly Assessment - Olurida_v090 Using Quast on Swoose

2021

Olympia Oyster Genome Assembly

After running a new Ostrea lurida assembly yesterday (Olurida_v090), I evaluated Olurida_v090 using Quast to produce some stats. This was run on my local computer with the…

<<<<<<< HEAD

I was recently tasked with adding annotations for our Ostrea lurida genome assembly to NCBI. As it turns out, adding just annotation files can’t be done since the genome was…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genome Assembly - Olurida_v090 with BGI Illumina and PacBio Hybrid Using Wengan on Mox

2021

Olympia Oyster Genome Assembly

May 20, 2021

I was recently tasked with adding annotations for our Ostrea lurida genome assembly to NCBI. As it turns out, adding just annotation files can’t be done since the genome was…

<<<<<<< HEAD

May 20, 2021

After attempting to submit our Ostrea lurida (Olympia oyster) genome assembly annotations (via GFF) to NCBI, the submission process also highlighted some short comings of the …

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Trimming - O.lurida BGI FastQs with FastP on Mox

fastp

mox

Ostrea lurida

Olympia oyster

trimming

2021

Olympia Oyster Genome Sequencing

May 18, 2021

After attempting to submit our Ostrea lurida (Olympia oyster) genome assembly annotations (via GFF) to NCBI, the submission process also highlighted some short comings of the …

<<<<<<< HEAD

May 18, 2021

Per this GitHub Issue, Steven has asked to get our Ostrea lurida (Olympia oyster) genome assembly (Olurida_v081.fa) submitted to NCBI with annotations. The first step in the…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genome Submission - Validation of Olurida_v081.fa and Annotated GFFs Prior to Submission to NCBI

2021

Olympia Oyster Genome Assembly

May 13, 2021

Per this GitHub Issue, Steven has asked to get our Ostrea lurida (Olympia oyster) genome assembly (Olurida_v081.fa) submitted to NCBI with annotations. The first step in the…

<<<<<<< HEAD

May 13, 2021

Decided to tackle this GitHub Issue about creating a transposable elements IGV track with the new Roslin C.gigas genome, since it had been sitting for a while and I have…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RepeatMasker - C.gigas Rosling NCBI Genome GCA_902806645.1 on Mox

GCA_902806645.1

mox

repeatmasker

Crassostrea gigas

Pacific oyster

2021

Miscellaneous

May 4, 2021

Decided to tackle this GitHub Issue about creating a transposable elements IGV track with the new Roslin C.gigas genome, since it had been sitting for a while and I have…

<<<<<<< HEAD

May 4, 2021

Aidan recently needed to use R on a machine with more memory. Additionally, it would be ideal if he could use RStudio. So, I managed to figure out how to set up a…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Singularity - RStudio Server Container on Mox

computing

Rstudio Server

mox

singularity

2021

Miscellaneous

Apr 23, 2021

Aidan recently needed to use R on a machine with more memory. Additionally, it would be ideal if he could use RStudio. So, I managed to figure out how to set up a…

<<<<<<< HEAD

Apr 23, 2021

To continue towards getting our Panopea generosa (Pacific geoduck) genome assembly (v1.0) analyzed with BlobToolKit, per this GitHub Issue, I’ve decided to run each aspect…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Read Mapping - 10x-Genomics Trimmed FastQ Mapped to P.generosa v1.0 Assembly Using Minimap2 for BlobToolKit on Mox

2021

Miscellaneous

To continue towards getting our Panopea generosa (Pacific geoduck) genome assembly (v1.0) analyzed with BlobToolKit, per this GitHub Issue, I’ve decided to run each aspect…

<<<<<<< HEAD

To continue towards getting our Panopea generosa (Pacific geoduck) genome assembly (v1.0) analyzed with BlobToolKit, per this GitHub Issue, I’ve decided to run each aspect…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genome Annotation - P.generosa v1.0 Assembly Using DIAMOND BLASTx for BlobToolKit on Mox

2021

Miscellaneous

To continue towards getting our Panopea generosa (Pacific geoduck) genome assembly (v1.0) analyzed with BlobToolKit, per this GitHub Issue, I’ve decided to run each aspect…

<<<<<<< HEAD

To continue towards getting our Panopea generosa (Pacific geoduck) genome assembly (v1.0) analyzed with BlobToolKit, per this GitHub Issue, I’ve decided to run each aspect…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genome Annotation - P.generosa v1.0 Assembly Using BLASTn for BlobToolKit on Mox

2021

Miscellaneous

To continue towards getting our Panopea generosa (Pacific geoduck) genome assembly (v1.0) analyzed with BlobToolKit, per this GitHub Issue, I’ve decided to run each aspect…

<<<<<<< HEAD

Steven asked me to try running Blob Tool Kit to identify potential contaminating sequence in our Panopea generosa (Pacific geoduck) genome assembly (v1.0). In preparation…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Trimming P.generosa 10x Genomics HiC FastQs with fastp on Mox

2021

Miscellaneous

Apr 1, 2021

Steven asked me to try running Blob Tool Kit to identify potential contaminating sequence in our Panopea generosa (Pacific geoduck) genome assembly (v1.0). In preparation…

<<<<<<< HEAD

Apr 1, 2021

Continued annotation of cbai_transcriptome_v4.0.fasta [Trinity de novo assembly from…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Annotation - Trinotate on C.bairdi Transcriptome v4.0 on Mox

2021

Miscellaneous

Continued annotation of cbai_transcriptome_v4.0.fasta [Trinity de novo assembly from…

<<<<<<< HEAD

Continued annotation of cbai_transcriptome_v4.0.fasta [Trinity de novo assembly from…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Annotation - DIAMOND BLASTx on C.bairdi Transcriptome v4.0 on Mox

2021

Miscellaneous

Continued annotation of cbai_transcriptome_v4.0.fasta [Trinity de novo assembly from…

<<<<<<< HEAD

Began annotation of cbai_transcriptome_v4.0.fasta Trinity de novo assembly from 20210317] using TransDecoder on Mox. This will be used as a component of Trinotate annotation…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

TransDecoder - C.bairdi Transcriptome v4.0 on Mox

2021

Tanner Crab RNAseq

Began annotation of cbai_transcriptome_v4.0.fasta Trinity de novo assembly from 20210317] using TransDecoder on Mox. This will be used as a component of Trinotate annotation…

<<<<<<< HEAD

I previously created a C.bairdi de novo transcriptome assembly v4.0 with Trinity from all our C.bairdi RNAseq reads which had BLASTx matches to the C.opilio genome and…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Assessment - BUSCO Metazoa on C.bairdi Transcriptome v4.0 on Mox

2021

Tanner Crab RNAseq

I previously created a C.bairdi de novo transcriptome assembly v4.0 with Trinity from all our C.bairdi RNAseq reads which had BLASTx matches to the C.opilio genome and…

<<<<<<< HEAD

Continuing to addressing this GitHub issue, to generate an additional C.bairdi transcriptome, I finally got to the point of actually running the assembly using Trinity using …

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Assembly - C.bairdi Transcriptome v4.0 Using Trinity on Mox

mox

Tanner crab

Chionoecetes bairdi

Trinity

transcriptome

assembly

RNAseq

2021

Tanner Crab RNAseq

Continuing to addressing this GitHub issue, to generate an additional C.bairdi transcriptome, I finally got to the point of actually running the assembly using Trinity using …

<<<<<<< HEAD

As part of addressing this GitHub issue, to generate an additional C.bairdi transcriptome, I needed to extract the reads ID’ed via BLASTX against the C.opilio genome on…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Read Extractions - C.bairdi RNAseq Reads from C.opilio BLASTx Matches with seqkit on Mox

2021

Tanner Crab RNAseq

Mar 16, 2021

As part of addressing this GitHub issue, to generate an additional C.bairdi transcriptome, I needed to extract the reads ID’ed via BLASTX against the C.opilio genome on…

<<<<<<< HEAD

Mar 16, 2021

We want to generate an additional Tanner crab (Chionoecetes bairdi) transcriptome, per this GitHub issue, to generate an additional C.bairdi transcriptome. This has come…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DIAMOND BLASTx - C.bairdi RNAseq vs C.opilio Genome Proteins on Mox

2021

Tanner Crab RNAseq

Mar 12, 2021

We want to generate an additional Tanner crab (Chionoecetes bairdi) transcriptome, per this GitHub issue, to generate an additional C.bairdi transcriptome. This has come…

<<<<<<< HEAD

Mar 12, 2021

To continue annotation of our Hematodinium v1.7 transcriptome assembly, I wanted to run Trinotate.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Annotation - Trinotate Hematodinium v1.7 on Mox

2021

Miscellaneous

To continue annotation of our Hematodinium v1.7 transcriptome assembly, I wanted to run Trinotate.

<<<<<<< HEAD

To continue annotation of our Hematodinium v1.6 transcriptome assembly, I wanted to run Trinotate.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Annotation - Trinotate Hematodinium v1.6 on Mox

2021

Miscellaneous

To continue annotation of our Hematodinium v1.6 transcriptome assembly, I wanted to run Trinotate.

<<<<<<< HEAD

I’d previously assembled hemat_transcriptome_v1.0.fasta on 20200122, hemat_transcriptome_v1.5.fasta on 20200408, extracted hemat_transcriptome_v2.1.fasta from an existing…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Assembly - Hematodinium Transcriptomes v1.6 and v1.7 with Trinity on Mox

Tanner crab

hematodinium

mox

trinity

Chionoecetes bairdi

2021

Miscellaneous

Mar 8, 2021

I’d previously assembled hemat_transcriptome_v1.0.fasta on 20200122, hemat_transcriptome_v1.5.fasta on 20200408, extracted hemat_transcriptome_v2.1.fasta from an existing…

<<<<<<< HEAD

Mar 8, 2021

Per this GitHub issue, Steven provided a list of methylation-related gene names and wanted to extract the corresponding Panopea generosa ([Pacific geoduck (Panopea generosa)]…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Wrangling - Gene ID Extraction from P.generosa Genome GFF Using Methylation Machinery Gene IDs

2021

Miscellaneous

Per this GitHub issue, Steven provided a list of methylation-related gene names and wanted to extract the corresponding Panopea generosa ([Pacific geoduck (Panopea generosa)]…

<<<<<<< HEAD

Per this GitHub Issue Steven asked that I take a list of gene names associated with DNA methylation and see if I could extract a list of Panopea generosa (Panopea generosa) g…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Wrangling - Gene ID Extraction from P.generosa Genome GFF Using Methylation Machinery List

2021

Miscellaneous

Per this GitHub Issue Steven asked that I take a list of gene names associated with DNA methylation and see if I could extract a list of Panopea generosa (Panopea generosa) g…

<<<<<<< HEAD

At the beginning of the month, Jay sent us his A.elegantissima ONT Fast5 data in order to help him get it submitted to NCBI Sequencing Read Archive (SRA).

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

SRA Submission - A.elegantissima ONT Fast5 from Jay Dimond

2021

SRA Submission

Feb 9, 2021

At the beginning of the month, Jay sent us his A.elegantissima ONT Fast5 data in order to help him get it submitted to NCBI Sequencing Read Archive (SRA).

<<<<<<< HEAD

Feb 9, 2021

Jay asked me to help get his A.elegantissima (aggregating anenome) NanoPore gDNA sequencing data submitted to NCBI Sequencing Read Archive (SRA). He sent a hard drive (HDD)…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Received - Anthopleura elegantissima - aggregating anenome - NanoPore Genome Sequence from Jay Dimond

2021

Miscellaneous

Feb 1, 2021

Jay asked me to help get his A.elegantissima (aggregating anenome) NanoPore gDNA sequencing data submitted to NCBI Sequencing Read Archive (SRA). He sent a hard drive (HDD)…

<<<<<<< HEAD

Feb 1, 2021

Submitted the M.magister MBD-BSseq libraries created 20201124 using the 4nM aliquots created for the MiSeq test run on 20201202 to the Univ. of Oregon GC3F sequencing core.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Samples Submitted - M.magister MBD-BSseq Libraries to Univ. of Oregon GC3F

Metacarcinus magister

sequencing

Dungeness crab

Cancer magister

2021

Miscellaneous

Jan 12, 2021

Submitted the M.magister MBD-BSseq libraries created 20201124 using the 4nM aliquots created for the MiSeq test run on 20201202 to the Univ. of Oregon GC3F sequencing core.

<<<<<<< HEAD

Jan 12, 2021

UPDATE: I’ll lead in with the fact that this failed with an error message that I can’t figure out. This will save the reader some time. I’ve posted the problem as an Issue…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Comparisons - C.bairdi Transcriptomes Evaluations with DETONATE rsem-eval on Mox

2020

Tanner Crab RNAseq

Dec 29, 2020

UPDATE: I’ll lead in with the fact that this failed with an error message that I can’t figure out. This will save the reader some time. I’ve posted the problem as an Issue…

<<<<<<< HEAD

Dec 29, 2020

I had previously attempted to compare all of our C.bairdi transcriptome assemblies using DETONATE on 20200601, but, due to hitting time limits on Mox, failed to successfully…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Alignments - C.bairdi RNAseq Transcriptome Alignments Using Bowtie2 on Mox

2020

Tanner Crab RNAseq

Dec 24, 2020

I had previously attempted to compare all of our C.bairdi transcriptome assemblies using DETONATE on 20200601, but, due to hitting time limits on Mox, failed to successfully…

<<<<<<< HEAD

Dec 24, 2020

Today we received the H & E-stained slides from the cockle clam gonad tissue blocks/cassettes we submitted on 20201201. Slides were added to Slide Case #5 - Rows 13 - 37 (Goo…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Samples Received - Cockle Clam Gonad H and E Slides

2020

Samples Received

Dec 17, 2020

Today we received the H & E-stained slides from the cockle clam gonad tissue blocks/cassettes we submitted on 20201201. Slides were added to Slide Case #5 - Rows 13 - 37 (Goo…

<<<<<<< HEAD

Dec 17, 2020

Earlier today we received the M.magister (C.magister; Dungeness crab) MiSeq data from Mac.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

FastQC-MultiQC - M.magister MBD-BSseq Pool Test MiSeq Run on Mox

2020

Miscellaneous

Earlier today we received the M.magister (C.magister; Dungeness crab) MiSeq data from Mac.

<<<<<<< HEAD

After creating _M.magister (C.magister; Dungeness crab) MBD-BSseq libraries (on 20201124), I gave the pooled set of samples to Mac for a test sequencing run on the MiSeq on…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Received - M.magister MBD-BSseq Pool Test MiSeq Run

2020

Miscellaneous

After creating _M.magister (C.magister; Dungeness crab) MBD-BSseq libraries (on 20201124), I gave the pooled set of samples to Mac for a test sequencing run on the MiSeq on…

<<<<<<< HEAD

Mac was getting some weird results when mapping some single cell RNAseq data to the C.gigas mitochondrial (mt) genome that she had, so she asked for some help mapping other C…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Alignment - C.gigas RNAseq to GCF_000297895.1_oyster_v9 Genome Using STAR on Mox

2020

Miscellaneous

Dec 8, 2020

Mac was getting some weird results when mapping some single cell RNAseq data to the C.gigas mitochondrial (mt) genome that she had, so she asked for some help mapping other C…

<<<<<<< HEAD

Dec 8, 2020

I submitted the 24 C.gigas diploid/triploid pH-treated WGBS sequence data we received 20201205 to the NCBI Sequence Read Archive (SRA).

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

SRA Submission - Haws Lab C.gigas Ploidy pH WGBS

2020

SRA Submission

Dec 7, 2020

I submitted the 24 C.gigas diploid/triploid pH-treated WGBS sequence data we received 20201205 to the NCBI Sequence Read Archive (SRA).

<<<<<<< HEAD

Dec 7, 2020

Making the assumption that the 24 C.gigas ploidy pH WGBS data we receved 20201205 will be analyzed using Bismark, I decided to go ahead and trim the files according to Bismark…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Trimming - Haws Lab C.gigas Ploidy pH WGBS 10bp 5 and 3 Prime Ends Using fastp and MultiQC on Mox

2020

Miscellaneous

Making the assumption that the 24 C.gigas ploidy pH WGBS data we receved 20201205 will be analyzed using Bismark, I decided to go ahead and trim the files according to Bismark…

<<<<<<< HEAD

[Yesterday (20201205), we received the whole genome bisulfite sequencing (WGBS) data back from…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

FastQC-MultiQc - C.gigas Ploidy pH WGBS Raw Sequence Data from Haws Lab on Mox

2020

Miscellaneous

[Yesterday (20201205), we received the whole genome bisulfite sequencing (WGBS) data back from…

<<<<<<< HEAD

Today we received the whole genome bisulfite sequencing (WGBS) from the 24 C.gigas diploid-triploid samples subjected to different pH that were submitted 20200824. The…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Received - C.gigas Diploid-Triploid pH Treatments Ctenidia WGBS from ZymoResearch

2020

Data Received

Dec 5, 2020

Today we received the whole genome bisulfite sequencing (WGBS) from the 24 C.gigas diploid-triploid samples subjected to different pH that were submitted 20200824. The…

<<<<<<< HEAD

Dec 5, 2020

Steven asked me to trim (GitHub Issue) Ronit’s WGBS sequencing data we received on 20201110, according to Bismark guidelines for libraries made with the ZymoResearch Pico…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Trimming - Ronits C.gigas Ploidy WGBS 10bp 5 and 3 Prime Ends Using fastp and MultiQC on Mox

2020

Miscellaneous

Steven asked me to trim (GitHub Issue) Ronit’s WGBS sequencing data we received on 20201110, according to Bismark guidelines for libraries made with the ZymoResearch Pico…

<<<<<<< HEAD

Earlier today I quantified the libraries with the Qubit in preparation for sample pooling and sequencing. Before performing a full sequencing run, Mac wanted to select a…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Sample Submission - M.magister MBD BSseq Libraries for MiSeq at NOAA

2020

Samples Submitted

Earlier today I quantified the libraries with the Qubit in preparation for sample pooling and sequencing. Before performing a full sequencing run, Mac wanted to select a…

<<<<<<< HEAD

After reviewing the Bionalyzer assays for the MBD BSseq libraries Mac indicated she’d like to have the libraries quantified using the Qubit.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Library Quantification - M.magister MBD BSseq Libraries with Qubit

2020

Miscellaneous

After reviewing the Bionalyzer assays for the MBD BSseq libraries Mac indicated she’d like to have the libraries quantified using the Qubit.

<<<<<<< HEAD

Per this GitHub Issue, Steven asked that I submit a set of fixed cockle clam gonad tissues (currently stored in histology cassettes in 70% EtOH) for Hematoxylin and eosin…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Samples Submitted - Cockle Clam Gonad Histology Cassettes for H and E

2020

Samples Submitted

Dec 1, 2020

Per this GitHub Issue, Steven asked that I submit a set of fixed cockle clam gonad tissues (currently stored in histology cassettes in 70% EtOH) for Hematoxylin and eosin…

<<<<<<< HEAD

Dec 1, 2020

Steven asked me to trim (GitHub Issue) Ronit’s WGBS sequencing data we received on 20201110, according to Bismark guidelines for libraries made with the ZymoResearch Pico…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Trimming - Ronits C.gigas Ploidy WGBS Using fastp and MultiQC on Mox

2020

Miscellaneous

Nov 30, 2020

Steven asked me to trim (GitHub Issue) Ronit’s WGBS sequencing data we received on 20201110, according to Bismark guidelines for libraries made with the ZymoResearch Pico…

<<<<<<< HEAD

Nov 30, 2020

MBD BSseq library construction was completed yesterday (20201124). Next, I needed to evaluate the libraries using the Roberts Lab Bioanalyzer 2100 (Agilent) to assess…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Bioanalyzer - M.magister MBD BSseq Libraries

2020

Miscellaneous

Nov 25, 2020

MBD BSseq library construction was completed yesterday (20201124). Next, I needed to evaluate the libraries using the Roberts Lab Bioanalyzer 2100 (Agilent) to assess…

<<<<<<< HEAD

Nov 25, 2020

After finishing the final set of eight MBD selections on 20201103, I’m finally ready to make the BSseq libraries using the Pico Methyl-Seq Library Prep Kit (ZymoResearch) (PD…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

MBD BSseq Library Prep - M.magister MBD-selected DNA Using Pico Methyl-Seq Kit

2020

Miscellaneous

Nov 24, 2020

After finishing the final set of eight MBD selections on 20201103, I’m finally ready to make the BSseq libraries using the Pico Methyl-Seq Library Prep Kit (ZymoResearch) (PD…

<<<<<<< HEAD

Nov 24, 2020

Shelly asked me to isolate RNA from some P.generosa hemocytes (GitHub Issue) that she had.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation and Quantification - P.generosa Hemocytes from Shelly

2020

Miscellaneous

Nov 19, 2020

Shelly asked me to isolate RNA from some P.generosa hemocytes (GitHub Issue) that she had.

<<<<<<< HEAD

Nov 19, 2020

A few days ago, we received the whole genome bisulfite sequencing (WBGS) data (20201110) from Ronit’s C.gigas diploid/triploid dessication/heat stress experiment (GitHub repo)…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

SRA Submission - Ronits C.gigas Ploidy WGBS

2020

SRA Submission

Nov 13, 2020

A few days ago, we received the whole genome bisulfite sequencing (WBGS) data (20201110) from Ronit’s C.gigas diploid/triploid dessication/heat stress experiment (GitHub repo)…

<<<<<<< HEAD

Nov 13, 2020

Earlier today, we received the C.gigas ploidy WGBS data that we submitted to ZymoResearch on 20200820.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

FastQC-MultiQc - C.gigas Ploidy WGBS Raw Sequence Data from Ronits Project on Mox

2020

Miscellaneous

Earlier today, we received the C.gigas ploidy WGBS data that we submitted to ZymoResearch on 20200820.

<<<<<<< HEAD

Grace was recently working on writing up a manuscript which did a basic comparison of our C.bairdi transcriptome (cbai_transcriptome_v3.1) (see the Genomic Resources wiki for…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Assessment - Crustacean Transcripome Completeness Evaluation Using BUSCO on Mox

2020

Miscellaneous

Grace was recently working on writing up a manuscript which did a basic comparison of our C.bairdi transcriptome (cbai_transcriptome_v3.1) (see the Genomic Resources wiki for…

<<<<<<< HEAD

We received the data from our whole genome bisulfite sequencing (WGBS) submission to ZymoResearch on 2020820 for Ronit’s C.gigas diploid/triploid dessication/heat stress…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Received - C.gigas Ploidy WGBS from Ronits Project via ZymoResearch

2020

Data Received

We received the data from our whole genome bisulfite sequencing (WGBS) submission to ZymoResearch on 2020820 for Ronit’s C.gigas diploid/triploid dessication/heat stress…

<<<<<<< HEAD

In Shelly’s GitHub Issue for this S.salar project, she also requested a MultiQC report for the trimming (completed on 20201029) and the genome alignments (completed on…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Wrangling - MultiQC on S.salar RNAseq from fastp and HISAT2 on Mox

2020

Miscellaneous

Nov 6, 2020

In Shelly’s GitHub Issue for this S.salar project, she also requested a MultiQC report for the trimming (completed on 20201029) and the genome alignments (completed on…

<<<<<<< HEAD

Nov 6, 2020

Completed upgrading the 12 x 8TB HDDs in our server, Gannet (Synology RS3618XS), to 12 x 16TB HDDs. The process was simple, but the repair process took ~20hrs for each new…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Hard Drive Upgrade - Gannet Synology Server

2020

Computer Servicing

Nov 5, 2020

Completed upgrading the 12 x 8TB HDDs in our server, Gannet (Synology RS3618XS), to 12 x 16TB HDDs. The process was simple, but the repair process took ~20hrs for each new…

<<<<<<< HEAD

Nov 5, 2020

This is a continuation of addressing Shelly Trigg’s (regarding some Salmo salar RNAseq data) request (GitHub Issue) to trim (completed 20201029), perform genome alignment (co…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNAseq Alignments - S.salar HISAT2 BAMs to GCF_000233375.1_ICSASG_v2_genomic.gtf Transcriptome Using StringTie on Mox

2020

Miscellaneous

Nov 4, 2020

This is a continuation of addressing Shelly Trigg’s (regarding some Salmo salar RNAseq data) request (GitHub Issue) to trim (completed 20201029), perform genome alignment (co…

<<<<<<< HEAD

Nov 4, 2020

This is a continuation of addressing Shelly Trigg’s (regarding some Salmo salar RNAseq data) request (GitHub Issue) to trim (completed 20201029), perform genome alignment…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNAseq Alignments - Trimmed S.salar RNAseq to GCF_000233375.1_ICSASG_v2_genomic.fa Using Hisat2 on Mox

2020

Miscellaneous

This is a continuation of addressing Shelly Trigg’s (regarding some Salmo salar RNAseq data) request (GitHub Issue) to trim (completed 20201029), perform genome alignment…

<<<<<<< HEAD

Click here for notebook on the first eight samples processed. Click here for the second set of eight samples processed. M.magister (Dungeness crab) gill gDNA provided by…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

MBD Selection - M.magister Sheared Gill gDNA 16 of 24 Samples Set 3 of 3

2020

Miscellaneous

Click here for notebook on the first eight samples processed. Click here for the second set of eight samples processed. M.magister (Dungeness crab) gill gDNA provided by…

<<<<<<< HEAD

Click here for notebook on the first eight samples processed. M.magister (Dungeness crab) gill gDNA provided by Mackenzie Gavery was previously sheared on 20201026 and three…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

MBD Selection - M.magister Sheared Gill gDNA 8 of 24 Samples Set 2 of 3

2020

Miscellaneous

Nov 2, 2020

Click here for notebook on the first eight samples processed. M.magister (Dungeness crab) gill gDNA provided by Mackenzie Gavery was previously sheared on 20201026 and three…

<<<<<<< HEAD

Nov 2, 2020

Shelly asked that I trim, align to a genome, and perform transcriptome alignment counts in this GitHub issue with some Salmo salar RNAseq data she had and, using a subset of…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Trimming - Shelly S.salar RNAseq Using fastp and MultiQC on Mox

2020

Miscellaneous

Oct 29, 2020

Shelly asked that I trim, align to a genome, and perform transcriptome alignment counts in this GitHub issue with some Salmo salar RNAseq data she had and, using a subset of…

<<<<<<< HEAD

Oct 29, 2020

M.magister (Dungeness crab) gill gDNA provided by Mackenzie Gavery was previously sheared on 20201026 and three samples were subjected to additional rounds of shearing on 202…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

MBD Selection - M.magister Sheared Gill gDNA 8 of 24 Samples Set 1 of 3

2020

Miscellaneous

Oct 28, 2020

M.magister (Dungeness crab) gill gDNA provided by Mackenzie Gavery was previously sheared on 20201026 and three samples were subjected to additional rounds of shearing on 202…

<<<<<<< HEAD

Oct 28, 2020

After shearing all of the M.magister gill gDNA on 20201026, there were still three samples that still had average fragment lengths that were a bit longer than desired…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Shearing - M.magister gDNA Additional Shearing CH05-01_21 CH07-11 and Bioanalyzer

2020

Miscellaneous

Oct 27, 2020

After shearing all of the M.magister gill gDNA on 20201026, there were still three samples that still had average fragment lengths that were a bit longer than desired…

<<<<<<< HEAD

Oct 27, 2020

I previously ran some shearing tests on 20201022 to determine how many cycles to run on the sonicator (Bioruptor 300; Diagenode) to achieve an average fragment length of…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Shearing - M.magister gDNA Shearing All Samples and Bioanalyzer

2020

Miscellaneous

Oct 26, 2020

I previously ran some shearing tests on 20201022 to determine how many cycles to run on the sonicator (Bioruptor 300; Diagenode) to achieve an average fragment length of…

<<<<<<< HEAD

Oct 26, 2020

Yesterday, I did some shearing of Metacarcinus magister gill gDNA on a test sample (CH05-21) to determine how many cycles to run on the sonicator (Bioruptor 300; Diagenode)…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Shearing - M.magister CH05-21 gDNA Full Shearing Test and Bioanalyzer

2020

Miscellaneous

Oct 22, 2020

Yesterday, I did some shearing of Metacarcinus magister gill gDNA on a test sample (CH05-21) to determine how many cycles to run on the sonicator (Bioruptor 300; Diagenode)…

<<<<<<< HEAD

Oct 22, 2020

Steven assigned me to do some MBD-BSseq library prep (GitHub Issue) for some Dungeness crab (Metacarcinus magister) DNA samples provided by Mackenzie Gavery. The DNA was…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Shearing - M.magister gDNA Shear Testing and Bioanalyzer

2020

Miscellaneous

Oct 21, 2020

Steven assigned me to do some MBD-BSseq library prep (GitHub Issue) for some Dungeness crab (Metacarcinus magister) DNA samples provided by Mackenzie Gavery. The DNA was…

<<<<<<< HEAD

Oct 21, 2020

After extracting FastQ reads using seqtk on 20201013 from the various taxa I had been interested in, the next thing needed doing was mapping reads to the cbai_genome_v1.01 “g…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Read Mapping - C.bairdi 201002558-2729-Q7 and 6129-403-26-Q7 Taxa-Specific NanoPore Reads to cbai_genome_v1.01.fasta Using Minimap2 on Mox

2020

Miscellaneous

Oct 14, 2020

After extracting FastQ reads using seqtk on 20201013 from the various taxa I had been interested in, the next thing needed doing was mapping reads to the cbai_genome_v1.01 “g…

<<<<<<< HEAD

Oct 14, 2020

In my pursuit to identify which contigs/scaffolds of our “C.bairdi” genome assembly from 20200917 correspond to interesting taxa, based on taxonomic assignments produced by…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Wrangling - C.bairdi NanoPore Reads Extractions With Seqtk on Mephisto

2020

Miscellaneous

Oct 13, 2020

In my pursuit to identify which contigs/scaffolds of our “C.bairdi” genome assembly from 20200917 correspond to interesting taxa, based on taxonomic assignments produced by…

<<<<<<< HEAD

Oct 13, 2020

After completing the taxonomic comparisons of 201002558-2729-Q7 and 6129-403-26-Q7 on 20201002, I decided to extract reads assigned to the following taxa for further…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

NanoPore Reads Extractions - C.bairdi Taxonomic Reads Extractions with MEGAN6 on 201002558-2729-Q7 and 6129-403-26-Q7

2020

Miscellaneous

Oct 7, 2020

After completing the taxonomic comparisons of 201002558-2729-Q7 and 6129-403-26-Q7 on 20201002, I decided to extract reads assigned to the following taxa for further…

<<<<<<< HEAD

Oct 7, 2020

After noticing that the initial MEGAN6 taxonomic assignments for our combined C.bairdi NanoPore data from 20200917 revealed a high number of bases assigned to E.canceri and A…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Comparison - C.bairdi 20102558-2729 vs. 6129-403-26 NanoPore Taxonomic Assignments Using MEGAN6

2020

Miscellaneous

Oct 2, 2020

After noticing that the initial MEGAN6 taxonomic assignments for our combined C.bairdi NanoPore data from 20200917 revealed a high number of bases assigned to E.canceri and A…

<<<<<<< HEAD

Oct 2, 2020

After noticing that the initial MEGAN6 taxonomic assignments for our combined C.bairdi NanoPore data from 20200917 revealed a high number of bases assigned to E.canceri and A…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Taxonomic Assignments - C.bairdi 6129-403-26-Q7 NanoPore Reads Using DIAMOND BLASTx on Mox and MEGAN6 daa2rma on emu

2020

Miscellaneous

After noticing that the initial MEGAN6 taxonomic assignments for our combined C.bairdi NanoPore data from 20200917 revealed a high number of bases assigned to E.canceri and A…

<<<<<<< HEAD

After noticing that the initial MEGAN6 taxonomic assignments for our combined C.bairdi NanoPore data from 20200917 revealed a high number of bases assigned to E.canceri and A…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Taxonomic Assignments - C.bairdi 20102558-2729-Q7 NanoPore Reads Using DIAMOND BLASTx on Mox and MEGAN6 daa2rma on emu

2020

Miscellaneous

After noticing that the initial MEGAN6 taxonomic assignments for our combined C.bairdi NanoPore data from 20200917 revealed a high number of bases assigned to E.canceri and A…

<<<<<<< HEAD

Last week, I ran all of our Q7-filtered C.baird NanoPore reads through MEGAN6 to evaluate the taxonomic breakdown (on 20200917) and noticed that there were a large quantity…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Wrangling - C.bairdi NanoPore 6129-403-26 Quality Filtering Using NanoFilt on Mox

2020

Miscellaneous

Last week, I ran all of our Q7-filtered C.baird NanoPore reads through MEGAN6 to evaluate the taxonomic breakdown (on 20200917) and noticed that there were a large quantity…

<<<<<<< HEAD

Last week, I ran all of our Q7-filtered C.baird NanoPore reads through MEGAN6 to evaluate the taxonomic breakdown (on 20200917) and noticed that there were a large quantity…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Wrangling - C.bairdi NanoPore 20102558-2729 Quality Filtering Using NanoFilt on Mox

2020

Miscellaneous

Last week, I ran all of our Q7-filtered C.baird NanoPore reads through MEGAN6 to evaluate the taxonomic breakdown (on 20200917) and noticed that there were a large quantity…

<<<<<<< HEAD

After creating a subset of the cbai_genome_v1.0 of contigs >100bp yesterday (subset named cbai_genome_v1.01), I wanted to generate BUSCO scores for cbai_genome_v1.01. This…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Assembly Assessment - BUSCO C.bairdi Genome v1.01 on Mox

2020

Miscellaneous

Sep 24, 2020

After creating a subset of the cbai_genome_v1.0 of contigs >100bp yesterday (subset named cbai_genome_v1.01), I wanted to generate BUSCO scores for cbai_genome_v1.01. This…

<<<<<<< HEAD

Sep 24, 2020

Previously assembled cbai_genome_v1.0.fasta with our NanoPore Q7 reads on 20200917 and noticed that there were numerous sequences that were well shorter than the expected…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Wrangling - Subsetting cbai_genome_v1.0 Assembly with faidx

2020

Miscellaneous

Sep 23, 2020

Previously assembled cbai_genome_v1.0.fasta with our NanoPore Q7 reads on 20200917 and noticed that there were numerous sequences that were well shorter than the expected…

<<<<<<< HEAD

Sep 23, 2020

Submitted our C.bairdi NanoPore sequencing data from 20200109 (Sample 20102558-2729 - uninfected EtOH-preserved muscle) and from 20200311 (Sample 6129_403_26 -…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

SRA Submissions - NanoPore C.bairdi 20102558-2729 and 6129_403_26

2020

SRA Submission

Sep 21, 2020

Submitted our C.bairdi NanoPore sequencing data from 20200109 (Sample 20102558-2729 - uninfected EtOH-preserved muscle) and from 20200311 (Sample 6129_403_26 -…

<<<<<<< HEAD

Sep 21, 2020

After using Flye to perform a de novo assembly of our Q7 filtered NanoPore sequencing data on 20200917, I decided to check the “completeness” of the assembly using BUSCO on…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Assembly Assessment - BUSCO C.bairdi Genome v1.0 on Mox

2020

Miscellaneous

Sep 18, 2020

After using Flye to perform a de novo assembly of our Q7 filtered NanoPore sequencing data on 20200917, I decided to check the “completeness” of the assembly using BUSCO on…

<<<<<<< HEAD

Sep 18, 2020

I previously converting our C.bairdi NanoPre sequencing data from the raw Fast5 format to FastQ format for our three sets of data:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Wrangling - C.bairdi NanoPore Quality Filtering Using NanoFilt on Mox

2020

Miscellaneous

I previously converting our C.bairdi NanoPre sequencing data from the raw Fast5 format to FastQ format for our three sets of data:

<<<<<<< HEAD

After quality filtering the C.bairdi NanoPore data earlier today, I performed a de novo assembly using Flye on Mox.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genome Assembly - C.bairdi - cbai_v1.0 - Using All NanoPore Data With Flye on Mox

2020

Genome Assembly

After quality filtering the C.bairdi NanoPore data earlier today, I performed a de novo assembly using Flye on Mox.

<<<<<<< HEAD

Earlier today I quality filtered (>=Q7) our C.baird NanoPore reads. One of the things I’d like to do now is to attempt to filter reads taxonomically, since the NanoPore data…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Taxonomic Assignments - C.bairdi NanoPore Reads Using DIAMOND BLASTx on Mox and MEGAN6 daa2rma on swoose

2020

Miscellaneous

Earlier today I quality filtered (>=Q7) our C.baird NanoPore reads. One of the things I’d like to do now is to attempt to filter reads taxonomically, since the NanoPore data…

<<<<<<< HEAD

On Monday (20200914), I checked a set of 28s and EF1a primer sets and determined that 28s-v4 and EF1a-v1 were probably the best of the bunch, although they all looked great.…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Geoduck Normalizing Gene Primers 28s-v4 and EF1a-v1 Tests

2020

Miscellaneous

Sep 16, 2020

On Monday (20200914), I checked a set of 28s and EF1a primer sets and determined that 28s-v4 and EF1a-v1 were probably the best of the bunch, although they all looked great.…

<<<<<<< HEAD

Sep 16, 2020

Shelly ordered some new primers (designed by Sam Gurr) (GitHub Issue) to potentially use as normalizing genes for her geoduck reproduction gene expression project and asked…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Geoduck Normalizing Gene Primer Checks

2020

Miscellaneous

Shelly ordered some new primers (designed by Sam Gurr) (GitHub Issue) to potentially use as normalizing genes for her geoduck reproduction gene expression project and asked…

<<<<<<< HEAD

I previously converting our C.bairdi NanoPre sequencing data from the raw Fast5 format to FastQ format for our three sets of data:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Wrangling - Visualization of C.bairdi NanoPore Sequencing Using NanoPlot on Mox

2020

Miscellaneous

I previously converting our C.bairdi NanoPre sequencing data from the raw Fast5 format to FastQ format for our three sets of data:

<<<<<<< HEAD

Time to start working with the NanoPore data that I generated back in March (???!!!). In order to proceed, I first need to convert the raw Fast5 files to FastQ. To do so…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Wrangling - NanoPore Fast5 Conversion to FastQ of C.bairdi 6129_403_26 on Mox with GPU Node

2020

Miscellaneous

Time to start working with the NanoPore data that I generated back in March (???!!!). In order to proceed, I first need to convert the raw Fast5 files to FastQ. To do so…

<<<<<<< HEAD

Continuing to work with the NanoPore data that I generated back in January(???!!!). In order to proceed, I first need to convert the raw Fast5 files to FastQ. To do so, I’ll…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Wrangling - NanoPore Fast5 Conversion to FastQ of C.bairdi 20102558-2729 Run-02 on Mox with GPU Node

2020

Miscellaneous

Continuing to work with the NanoPore data that I generated back in January(???!!!). In order to proceed, I first need to convert the raw Fast5 files to FastQ. To do so, I’ll…

<<<<<<< HEAD

Time to start working with the NanoPore data that I generated back in January(???!!!). In order to proceed, I first need to convert the raw Fast5 files to FastQ. To do so…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Wrangling - NanoPore Fast5 Conversion to FastQ of C.bairdi 20102558-2729 Run-01 on Mox with GPU Node

2020

Miscellaneous

Time to start working with the NanoPore data that I generated back in January(???!!!). In order to proceed, I first need to convert the raw Fast5 files to FastQ. To do so…

<<<<<<< HEAD

I re-quantified samples for Zymo whole genome bisulfite sequencing (WGBS) project 3534 earlier today due to ZymoResearch indicating there was insufficient DNA for most of…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Samples Submission - Supplemental Ronits C.gigas Diploid-Triploid Ctendidia gDNA for WGBS by ZymoResearch

2020

Samples Submitted

I re-quantified samples for Zymo whole genome bisulfite sequencing (WGBS) project 3534 earlier today due to ZymoResearch indicating there was insufficient DNA for most of…

<<<<<<< HEAD

I received notice from ZymoResearch yesterday afternoon that the DNA we sent on 20200820 for this project (Quote 3534) had insufficient DNA for sequencing for most of the…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Quantification - Re-quant Ronits C.gigas Diploid-Triploid Ctenidia gDNA Submitted to ZymoResearch

2020

Miscellaneous

I received notice from ZymoResearch yesterday afternoon that the DNA we sent on 20200820 for this project (Quote 3534) had insufficient DNA for sequencing for most of the…

<<<<<<< HEAD

To continue annotation of our C.bairdi v2.1 transcriptome assembly], I wanted to run Trinotate.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Annotation - Trinotate C.bairdi v2.1 on Mox

2020

Tanner Crab RNAseq

Aug 31, 2020

To continue annotation of our C.bairdi v2.1 transcriptome assembly], I wanted to run Trinotate.

<<<<<<< HEAD

Aug 31, 2020

To continue annotation of our C.bairdi v3.1 transcriptome assembly], I wanted to run Trinotate.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Annotation - Trinotate C.bairdi v3.1 on Mox

2020

Tanner Crab RNAseq

Aug 28, 2020

To continue annotation of our C.bairdi v3.1 transcriptome assembly], I wanted to run Trinotate.

<<<<<<< HEAD

Aug 28, 2020

To continue annotation of our Hematodinium v3.1 transcriptome assembly, I wanted to run Trinotate.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Annotation - Trinotate Hematodinium v3.1 on Mox

2020

Miscellaneous

To continue annotation of our Hematodinium v3.1 transcriptome assembly, I wanted to run Trinotate.

<<<<<<< HEAD

To continue annotation of our Hematodinium v1.6 transcriptome assembly, I wanted to run Trinotate.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Annotation - Trinotate Hematodinium v2.1 on Mox

2020

Miscellaneous

To continue annotation of our Hematodinium v1.6 transcriptome assembly, I wanted to run Trinotate.

<<<<<<< HEAD

To continue annotation of our C.bairdi v2.1 & v3.1 transcriptome assemblies, I needed to run TransDecoder before performing the more thorough annotation with Trinotate.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

TransDecoder - C.bairdi Transcriptomes v2.1 and v3.1 on Mox

2020

Tanner Crab RNAseq

To continue annotation of our C.bairdi v2.1 & v3.1 transcriptome assemblies, I needed to run TransDecoder before performing the more thorough annotation with Trinotate.

<<<<<<< HEAD

After testing out the RPL5 and TIF3s6b v2 and v3 primers yesterday on pooled cDNA, we determined the primers looked good, so will go forward testing them on a set of P.genero…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - P.generosa RPL5 and TIF3s6b v2 and v3 Normalizing Gene Assessment

2020

Miscellaneous

Aug 25, 2020

After testing out the RPL5 and TIF3s6b v2 and v3 primers yesterday on pooled cDNA, we determined the primers looked good, so will go forward testing them on a set of P.genero…

<<<<<<< HEAD

Aug 25, 2020

Submitted 1.5ug of the 24 C.gigas ctenidia ctenidia gDNA isolated last week (20200821) to ZymoResearch for whole genome bisulfite sequencing (WGBS) to compare differences in…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Sample Submitted - C.gigas Diploid-Triploid pH Treatments Ctenidia to ZymoResearch for WGBS

2020

Miscellaneous

Submitted 1.5ug of the 24 C.gigas ctenidia ctenidia gDNA isolated last week (20200821) to ZymoResearch for whole genome bisulfite sequencing (WGBS) to compare differences in…

<<<<<<< HEAD

Shelly ordered some new primers as potential normalizing genes and asked me to test them out (GitHub Issue).

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - P.generosa RPL5-v2-v3 and TIF3s6b-v2-v3 Primer Tests

2020

Miscellaneous

Shelly ordered some new primers as potential normalizing genes and asked me to test them out (GitHub Issue).

<<<<<<< HEAD

Isolated DNA from 24 of the Crassostrea gigas high/low pH triploid/diploid ctenidia samples that we received yesterday from the Haws Lab. Samples selected by Steven.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Isolation and Quantification - C.gigas High-Low pH Triploid and Diploid Ctenidia

2020

Miscellaneous

Aug 21, 2020

Isolated DNA from 24 of the Crassostrea gigas high/low pH triploid/diploid ctenidia samples that we received yesterday from the Haws Lab. Samples selected by Steven.

<<<<<<< HEAD

Aug 21, 2020

Received Crassostrea gigas tissue samples from Maria Haws’ Lab at the University of Hawaii Hilo. Tissue samples are a set of triploid and diploid subjected to different pHs.…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Samples Received - C.gigas High-Low pH Triploid Diploid from Maria Haws Lab

2020

Samples Received

Received Crassostrea gigas tissue samples from Maria Haws’ Lab at the University of Hawaii Hilo. Tissue samples are a set of triploid and diploid subjected to different pHs.…

<<<<<<< HEAD

Submitted 1.75ug of gDNA from 10 Crassostrea gigas ctenidia samples from Ronit’s dessication/temp/ploidy experiment to ZymoResearch for whole genome bisulfite sequencing…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Samples Submitted - Ronits C.gigas Diploid and Triploid Ctenidia to ZymoResearch for WGBS

2020

Miscellaneous

Submitted 1.75ug of gDNA from 10 Crassostrea gigas ctenidia samples from Ronit’s dessication/temp/ploidy experiment to ZymoResearch for whole genome bisulfite sequencing…

<<<<<<< HEAD

Realized that transcriptomes v2.1 and v3.1 (extracted from BLASTx-annotated FastAs from 20200605) didn’t have any associated stats.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Assembly Stats - C.bairdi Transcriptomes v2.1 and v3.1 Trinity Stats on Mox

2020

Miscellaneous

Aug 19, 2020

Realized that transcriptomes v2.1 and v3.1 (extracted from BLASTx-annotated FastAs from 20200605) didn’t have any associated stats.

<<<<<<< HEAD

Aug 19, 2020

Steven asked me to trim Roberto’s C.gigas whole genome bisulfite sequencing (WGBS) reads (GitHub Issue) “following his methods”. The only thing specified is trimming…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Trimming-FastQC-MultiQC - Robertos C.gigas WGBS FastQ Data with fastp FastQC and MultiQC on Mox

2020

Miscellaneous

Aug 18, 2020

Steven asked me to trim Roberto’s C.gigas whole genome bisulfite sequencing (WGBS) reads (GitHub Issue) “following his methods”. The only thing specified is trimming…

<<<<<<< HEAD

Aug 18, 2020

To continue annotation of our Hematodinium v1.6, v1.7, v2.1 & v3.1 transcriptome assemblies, I needed to run TransDecoder before performing the more thorough annotation with …

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

TransDecoder - Hematodinium Transcriptomes v1.6, v1.7, v2.1 and v3.1 on Mox

2020

Miscellaneous

To continue annotation of our Hematodinium v1.6, v1.7, v2.1 & v3.1 transcriptome assemblies, I needed to run TransDecoder before performing the more thorough annotation with …

<<<<<<< HEAD

Working on dealing with our various cbaiodinium sp. transcriptomes and realized that transcriptomes v2.1 and v3.1 (extracted from BLASTx-annotated FastAs from 20200605)…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Assembly Stats - cbaiodinium Transcriptomes v2.1 and v3.1 Trinity Stats on Mox

2020

Miscellaneous

Working on dealing with our various cbaiodinium sp. transcriptomes and realized that transcriptomes v2.1 and v3.1 (extracted from BLASTx-annotated FastAs from 20200605)…

<<<<<<< HEAD

Needed to assess the Hematodinium sp. transcriptomes that I’ve assembled to determine their “completeness” using BUSCO.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Assessment - BUSCO Metazoa on Hematodinium v1.6 v1.7 v2.1 and v3.1 on Mox

2020

Miscellaneous

Needed to assess the Hematodinium sp. transcriptomes that I’ve assembled to determine their “completeness” using BUSCO.

<<<<<<< HEAD

Needed to annotate the Hematodinium sp. transcriptomes that I’ve assembled using DIAMOND BLASTx. This will also be used for additional downstream annotation (TransDecoder…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Annotation - Hematodinium Transcriptomes v1.6 v1.7 v2.1 v3.1 with DIAMOND BLASTx on Mox

2020

Miscellaneous

Needed to annotate the Hematodinium sp. transcriptomes that I’ve assembled using DIAMOND BLASTx. This will also be used for additional downstream annotation (TransDecoder…

<<<<<<< HEAD

Shelly asked me to run some qPCRs (GitHub Issue), after some of the qPCR results I got from primer tests with normalzing genes and potential gene targets.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - P.generosa APLP and TIF3s8-1 with cDNA

2020

Miscellaneous

Aug 6, 2020

Shelly asked me to run some qPCRs (GitHub Issue), after some of the qPCR results I got from primer tests with normalzing genes and potential gene targets.

<<<<<<< HEAD

Aug 6, 2020

Continuing working on the manuscript for this data, Emma wanted the number of reads aligned to each gene. I previously created and assembly with genes/proteins using…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

FastQ Read Alignment and Quantification - P.generosa Water Metagenomic Libraries to MetaGeneMark Assembly with Hisat2 on Mox

2020

Miscellaneous

Jul 31, 2020

Continuing working on the manuscript for this data, Emma wanted the number of reads aligned to each gene. I previously created and assembly with genes/proteins using…

<<<<<<< HEAD

Jul 31, 2020

Shelly asked that I re-run the primer design pipeline that Kaitlyn had previously run to design a set of reproduction-related qPCR primers. Unfortunately, Kaitlyn’s Jupyter…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Primer Design and In-Silico Testing - Geoduck Reproduction Primers

2020

Miscellaneous

Jul 30, 2020

Shelly asked that I re-run the primer design pipeline that Kaitlyn had previously run to design a set of reproduction-related qPCR primers. Unfortunately, Kaitlyn’s Jupyter…

<<<<<<< HEAD

Jul 30, 2020

Ran some qPCRs on some other primers on 20200723 and then Shelly has asked me to test some additional qPCR primers that might have acceptable melt curves and be usable as…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Testing P.generosa Reproduction-related Primers

2020

Miscellaneous

Jul 29, 2020

Ran some qPCRs on some other primers on 20200723 and then Shelly has asked me to test some additional qPCR primers that might have acceptable melt curves and be usable as…

<<<<<<< HEAD

Jul 29, 2020

Added our P.generosa metagenomics sequencing data to NCBI sequencing read archive (SRA).

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

SRA Submission - P.generosa Metagenomics Data

2020

Miscellaneous

Jul 27, 2020

Added our P.generosa metagenomics sequencing data to NCBI sequencing read archive (SRA).

<<<<<<< HEAD

Jul 27, 2020

Shelly has asked me to test some qPCR primers related to geoduck reproduction.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Testing P.generosa Reproduction-related Primers

2020

Miscellaneous

Jul 23, 2020

Shelly has asked me to test some qPCR primers related to geoduck reproduction.

<<<<<<< HEAD

Jul 23, 2020

Isolated some gDNA from the triploid Nisbet oysters we received on 20200218 and one of Ronit’s diploid ctenidia samples (Google Sheet) using the E.Z.N.A. Mollusc DNA Kit…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Isolation and Quantification - C.gigas Diploid (Ronit) and Triploid (Nisbet)

2020

Miscellaneous

Jul 22, 2020

Isolated some gDNA from the triploid Nisbet oysters we received on 20200218 and one of Ronit’s diploid ctenidia samples (Google Sheet) using the E.Z.N.A. Mollusc DNA Kit…

<<<<<<< HEAD

Jul 22, 2020

Can’t remember where it was discussed (probably lab meeting), but I created a GitHub Issue to add all of geoduck RNAseq data to NCBI Short Read Archive (SRA). Anyway, got…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

SRA Submission - Geoduck Epigenetic Ocean Acidification RNAseq

2020

SRA Submission

Jul 9, 2020

Can’t remember where it was discussed (probably lab meeting), but I created a GitHub Issue to add all of geoduck RNAseq data to NCBI Short Read Archive (SRA). Anyway, got…

<<<<<<< HEAD

Jul 9, 2020

Submitted our Ostrea lurida v081 genome assembly FastA to the European Nucloetide Archive.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

ENA Submission - Ostrea lurida draft genome Olurida_v081.fa

2020

Olympia Oyster Genome Sequencing

Jul 8, 2020

Submitted our Ostrea lurida v081 genome assembly FastA to the European Nucloetide Archive.

<<<<<<< HEAD

Jul 8, 2020

Decided to finally take the time to methodically extract data from our metagenomics project so that I have the tables handy when I need them and I can easily share them with…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Metagenomics - Data Extractions Using MEGAN6

2020

Miscellaneous

Jun 18, 2020

Decided to finally take the time to methodically extract data from our metagenomics project so that I have the tables handy when I need them and I can easily share them with…

<<<<<<< HEAD

Jun 18, 2020

Decided to annotate the two C.bairdi transcriptomes , cbai_transcriptome_v2.1 and cbai_transcriptome_v3.1, generated on 20200605 using DIAMOND BLASTx on Mox.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Annotation - C.bairdi Transcriptomes v2.1 and v3.1 Using DIAMOND BLASTx on Mox

2020

Miscellaneous

Jun 8, 2020

Decided to annotate the two C.bairdi transcriptomes , cbai_transcriptome_v2.1 and cbai_transcriptome_v3.1, generated on 20200605 using DIAMOND BLASTx on Mox.

<<<<<<< HEAD

Jun 8, 2020

Continuing to try to identify the best C.bairdi transcriptome, we decided to extract all non-dinoflagellate sequences from cbai_transcriptome_v2.0 (RNAseq shorthand: 2018…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Assessment - BUSCO Metazoa on C.bairdi Transcriptome v3.1

2020

Miscellaneous

Continuing to try to identify the best C.bairdi transcriptome, we decided to extract all non-dinoflagellate sequences from cbai_transcriptome_v2.0 (RNAseq shorthand: 2018…

<<<<<<< HEAD

Continuing to try to identify the best C.bairdi transcriptome, we decided to extract all non-dinoflagellate sequences from cbai_transcriptome_v2.0 (RNAseq shorthand: 2018…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Assessment - BUSCO Metazoa on C.bairdi Transcriptome v2.1

2020

Miscellaneous

Continuing to try to identify the best C.bairdi transcriptome, we decided to extract all non-dinoflagellate sequences from cbai_transcriptome_v2.0 (RNAseq shorthand: 2018…

<<<<<<< HEAD

Continuing to try to identify the best C.bairdi transcriptome, we decided to extract all non-dinoflagellate sequences from cbai_transcriptome_v2.0 (RNAseq shorthand: 2018…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Sequence Extractions - C.bairdi Transcriptomes v2.0 and v3.0 Excluding Alveolata with MEGAN6 on Swoose

2020

Miscellaneous

Continuing to try to identify the best C.bairdi transcriptome, we decided to extract all non-dinoflagellate sequences from cbai_transcriptome_v2.0 (RNAseq shorthand: 2018…

<<<<<<< HEAD

Continuing to try to identify the best C.bairdi transcriptome, we decided to extract all non-dinoflagellate sequences from cbai_transcriptome_v2.0 (RNAseq shorthand: 2018…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Annotation - C.bairdi Transcriptomes v2.0 and v3.0 with DIAMOND BLASTx on Mox

2020

Miscellaneous

Jun 4, 2020

Continuing to try to identify the best C.bairdi transcriptome, we decided to extract all non-dinoflagellate sequences from cbai_transcriptome_v2.0 (RNAseq shorthand: 2018…

<<<<<<< HEAD

Jun 4, 2020

Attempting to get some other metrics regarding our various C.bairdi transcriptome assemblies other than BUSCO scores, I decided to try running DETONATE, as this is a…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Comparison - C.bairdi Transcriptomes Evaluations with DETONATE on Mox

2020

Miscellaneous

Jun 1, 2020

Attempting to get some other metrics regarding our various C.bairdi transcriptome assemblies other than BUSCO scores, I decided to try running DETONATE, as this is a…

<<<<<<< HEAD

Jun 1, 2020

We’ve produced a number of C.bairdi transcriptomes and we’re interested in doing some comparisons to try to determine which one might be “best”. I previously compared the…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Comparison - C.bairdi Transcriptomes Compared with DETONATE on Mox

2020

Miscellaneous

We’ve produced a number of C.bairdi transcriptomes and we’re interested in doing some comparisons to try to determine which one might be “best”. I previously compared the…

<<<<<<< HEAD

After creating a de novo assembly of C.bairdi transcriptome v1.7 on 20200527, performing BLASTx annotation on 202000527, and TransDecoder for ORF identification on 20200527…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Annotation - Trinotate C.bairdi Transcriptome-v1.7 on Mox

2020

Miscellaneous

After creating a de novo assembly of C.bairdi transcriptome v1.7 on 20200527, performing BLASTx annotation on 202000527, and TransDecoder for ORF identification on 20200527…

<<<<<<< HEAD

Since we’ve generated a number of versions of the C.bairdi transcriptome, we’ve decided to compare them using various metrics. Here, I’ve compared the BUSCO scores generated…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Comparisons - C.bairdi BUSCO Scores

2020

Miscellaneous

May 28, 2020

Since we’ve generated a number of versions of the C.bairdi transcriptome, we’ve decided to compare them using various metrics. Here, I’ve compared the BUSCO scores generated…

<<<<<<< HEAD

May 28, 2020

Need to run TransDecoder on Mox on the C.bairdi transcriptome v1.7 from 20200527.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

TransDecoder - C.bairdi Transcriptome v1.7 on Mox

2020

Miscellaneous

Need to run TransDecoder on Mox on the C.bairdi transcriptome v1.7 from 20200527.

<<<<<<< HEAD

As part of annotating cbai_transcriptome_v1.7.fasta from 20200527, I need to run DIAMOND BLASTx to use with Trinotate.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Annotation - C.bairdi Transcriptome v1.7 Using DIAMOND BLASTx on Mox

2020

Miscellaneous

As part of annotating cbai_transcriptome_v1.7.fasta from 20200527, I need to run DIAMOND BLASTx to use with Trinotate.

<<<<<<< HEAD

I previously created a C.bairdi de novo transcriptome assembly v1.7 with Trinity from all our C.bairdi taxonomically filtered pooled RNAseq samples on 20200527 and decided…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Assessment - BUSCO Metazoa on C.bairdi Transcriptome v1.7

2020

Miscellaneous

I previously created a C.bairdi de novo transcriptome assembly v1.7 with Trinity from all our C.bairdi taxonomically filtered pooled RNAseq samples on 20200527 and decided…

<<<<<<< HEAD

For completeness sake, I wanted to create an additional C.bairdi transcriptome assembly that consisted of Arthropoda only sequences from just pooled RNAseq data (since I rece…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Assembly - C.bairdi All Pooled Arthropoda-only RNAseq Data with Trinity on Mox

2020

Miscellaneous

For completeness sake, I wanted to create an additional C.bairdi transcriptome assembly that consisted of Arthropoda only sequences from just pooled RNAseq data (since I rece…

<<<<<<< HEAD

After performing de novo assembly on all of our Tanner crab RNAseq data (no taxonomic filter applied, either) on 20200518, I continued the annotation process by running Trino…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Annotation - Trinotate C.bairdi Transcriptome-v3.0 on Mox

2020

Miscellaneous

May 26, 2020

After performing de novo assembly on all of our Tanner crab RNAseq data (no taxonomic filter applied, either) on 20200518, I continued the annotation process by running Trino…

<<<<<<< HEAD

May 26, 2020

After generating a number of C.bairdi (Tanner crab) transcriptomes, we decided we should compare them to evaluate which to help decide which one should become our…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Assembly - P.trituberculatus (Japanese blue crab) NCBI SRA BioProject PRJNA597187 Data with Trinity on Mox

2020

Miscellaneous

May 23, 2020

After generating a number of C.bairdi (Tanner crab) transcriptomes, we decided we should compare them to evaluate which to help decide which one should become our…

<<<<<<< HEAD

May 23, 2020

We’ve produced a number of C.bairid transcriptomes utilizing different assembly approaches (e.g. Arthropoda reads only, stranded libraries only, mixed strandedness…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

SRA Library Assessment - Determine RNAseq Library Strandedness from P.trituberculatus SRA BioProject PRJNA597187

2020

Miscellaneous

We’ve produced a number of C.bairid transcriptomes utilizing different assembly approaches (e.g. Arthropoda reads only, stranded libraries only, mixed strandedness…

<<<<<<< HEAD

I was looking for some crab transcriptomic data today and, unable to find any previously assembled transcriptomes, turned to the good ol’ NCBI SRA. In order to simplify…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Tutorial - SRA Toolkit for Data Retrieval and Conversion to FastQ

2020

Tutorials

I was looking for some crab transcriptomic data today and, unable to find any previously assembled transcriptomes, turned to the good ol’ NCBI SRA. In order to simplify…

<<<<<<< HEAD

After creating a de novo assembly of C.bairdi transcriptome v1.6 on 20200518, performing BLASTx annotation on 202000519, and TransDecoder for ORF identification on 20200519…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Annotation - Trinotate C.bairdi Transcriptome-v1.6 on Mox

2020

Miscellaneous

May 20, 2020

After creating a de novo assembly of C.bairdi transcriptome v1.6 on 20200518, performing BLASTx annotation on 202000519, and TransDecoder for ORF identification on 20200519…

<<<<<<< HEAD

May 20, 2020

Need to run TransDecoder on Mox on the C.bairdi transcriptome v1.6 from 20200518.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

TransDecoder - C.bairdi Transcriptome v1.6 on Mox

2020

Miscellaneous

Need to run TransDecoder on Mox on the C.bairdi transcriptome v1.6 from 20200518.

<<<<<<< HEAD

Need to run TransDecoder on Mox on the C.bairdi transcriptome v3.0 from 20200518.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

TransDecoder - C.bairdi Transcriptome v3.0 from 20200518 on Mox

2020

Miscellaneous

Need to run TransDecoder on Mox on the C.bairdi transcriptome v3.0 from 20200518.

<<<<<<< HEAD

As part of annotating cbai_transcriptome_v1.6.fasta from 20200518, I need to run DIAMOND BLASTx to use with Trinotate.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Annotation - C.bairdi Transcriptome v1.6 Using DIAMOND BLASTx on Mox

2020

Miscellaneous

As part of annotating cbai_transcriptome_v1.6.fasta from 20200518, I need to run DIAMOND BLASTx to use with Trinotate.

<<<<<<< HEAD

I previously created a C.bairdi de novo transcriptome assembly v1.6 with Trinity from all our C.bairdi taxonomically filtered RNAseq on 20200518 and decided to assess its…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Assessment - BUSCO Metazoa on C.bairdi Transcriptome v1.6

2020

Miscellaneous

I previously created a C.bairdi de novo transcriptome assembly v1.6 with Trinity from all our C.bairdi taxonomically filtered RNAseq on 20200518 and decided to assess its…

<<<<<<< HEAD

As part of annotating cbai_transcriptome_v3.0.fasta from 20200518, I need to run DIAMOND BLASTx to use with Trinotate.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Annotation - C.bairdi Transcriptome v3.0 Using DIAMOND BLASTx on Mox

2020

Miscellaneous

As part of annotating cbai_transcriptome_v3.0.fasta from 20200518, I need to run DIAMOND BLASTx to use with Trinotate.

<<<<<<< HEAD

I previously created a C.bairdi de novo transcriptome assembly with Trinity from all our C.bairdi pooled RNAseq (not taxonomically filtered) on 20200518 and decided to…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Assessment - BUSCO Metazoa on C.bairdi Transcriptome v3.0

2020

Miscellaneous

I previously created a C.bairdi de novo transcriptome assembly with Trinity from all our C.bairdi pooled RNAseq (not taxonomically filtered) on 20200518 and decided to…

<<<<<<< HEAD

I realized I hadn’t performed taxonomic read separation from one set of RNAseq data we had. And, since I was on a transcriptome assembly kick, I figured I’d generate another …

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Assembly - C.bairdi All Arthropoda-specific RNAseq Data with Trinity on Mox

2020

Miscellaneous

I realized I hadn’t performed taxonomic read separation from one set of RNAseq data we had. And, since I was on a transcriptome assembly kick, I figured I’d generate another …

<<<<<<< HEAD

After using MEGAN6 to extract Arthropoda and Alveolata reads from our RNAseq data on 20200114, I had then extracted taxonomic-specific reads and aggregated each into basic…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Wrangling - Arthropoda and Alveolata D26 Pool RNAseq FastQ Extractions

2020

Miscellaneous

After using MEGAN6 to extract Arthropoda and Alveolata reads from our RNAseq data on 20200114, I had then extracted taxonomic-specific reads and aggregated each into basic…

<<<<<<< HEAD

Steven asked that I assemble a transcriptome with just our pooled C.bairdi RNAseq data (not taxonomically filtered; see the FastQ list file linked in the Results section…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Assembly - C.bairdi All Pooled RNAseq Data Without Taxonomic Filters with Trinity on Mox

2020

Miscellaneous

Steven asked that I assemble a transcriptome with just our pooled C.bairdi RNAseq data (not taxonomically filtered; see the FastQ list file linked in the Results section…

<<<<<<< HEAD

After performing de novo assembly on all of our Tanner crab RNAseq data (no taxonomic filter applied, either) on 20200502 and performing BLASTx annotation on 20200508, I…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Annotation - Trinotate C.bairdi Transcriptome v2.0 from 20200502 on Mox

2020

Miscellaneous

May 13, 2020

After performing de novo assembly on all of our Tanner crab RNAseq data (no taxonomic filter applied, either) on 20200502 and performing BLASTx annotation on 20200508, I…

<<<<<<< HEAD

May 13, 2020

Need to run TransDecoder on Mox on the C.bairdi transcriptome v2.0 from 20200502.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

TransDecoder - C.bairdi Transcriptome v2.0 from 20200502 on Mox

2020

Miscellaneous

Need to run TransDecoder on Mox on the C.bairdi transcriptome v2.0 from 20200502.

<<<<<<< HEAD

As part of annotating the C.bairdi v2.0 transcriptome assembly from 20200502, I need to run DIAMOND BLASTx to use with Trinotate.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Annotation - C.bairdi Transcriptome v2.0 Using DIAMOND BLASTx on Mox

2020

Miscellaneous

As part of annotating the C.bairdi v2.0 transcriptome assembly from 20200502, I need to run DIAMOND BLASTx to use with Trinotate.

<<<<<<< HEAD

I previously created a C.bairdi de novo transcriptome assembly with Trinity using all existing, unfiltered (i.e. no taxonomic selection) RNAseq data on 20200502 and decided…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Assessment - BUSCO Metazoa on C.bairdi v2.0 Transcriptome

2020

Miscellaneous

I previously created a C.bairdi de novo transcriptome assembly with Trinity using all existing, unfiltered (i.e. no taxonomic selection) RNAseq data on 20200502 and decided…

<<<<<<< HEAD

Steven asked that I assemble an unfiltered (i.e. no taxonomic selection) transcriptome with all of our C.bairdi RNAseq data (see the FastQ list file linked in the Results…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Assembly - C.bairdi All RNAseq Data Without Taxonomic Filters with Trinity on Mox

2020

Miscellaneous

May 2, 2020

Steven asked that I assemble an unfiltered (i.e. no taxonomic selection) transcriptome with all of our C.bairdi RNAseq data (see the FastQ list file linked in the Results…

<<<<<<< HEAD

May 2, 2020

Clarified with Steven an approach for tackling multi-condition comparisons (see this GitHub Issue). As such, I need to have individual transcript abundances for each sample…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcript Abundance - C.bairdi Alignment-free with Salmon Using 2020-GW Data on Mox

2020

Miscellaneous

Apr 29, 2020

Clarified with Steven an approach for tackling multi-condition comparisons (see this GitHub Issue). As such, I need to have individual transcript abundances for each sample…

<<<<<<< HEAD

Apr 29, 2020

After running pairwise comparisons and identify differentially expressed genes (DEGs) on 20200422 and finding enriched gene ontology terms, I decided to map the GO terms to…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

GO to GOslim - C.bairdi Enriched GO Terms from 20200422 DEGs

2020

Miscellaneous

Apr 27, 2020

After running pairwise comparisons and identify differentially expressed genes (DEGs) on 20200422 and finding enriched gene ontology terms, I decided to map the GO terms to…

<<<<<<< HEAD

Apr 27, 2020

Laura Spencer received her O.lurida QuantSeq data, so I put it through FastQC/MultiQC and put the pertinent info in the nightingales Google Sheet. I also moved the data to /o…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

FastQC-MultiQC - Laura Spencer’s QuantSeq Data

2020

Miscellaneous

Apr 26, 2020

Laura Spencer received her O.lurida QuantSeq data, so I put it through FastQC/MultiQC and put the pertinent info in the nightingales Google Sheet. I also moved the data to /o…

<<<<<<< HEAD

Apr 26, 2020

Per a Slack request, Steven asked me to take the Genewize RNAseq data (received 2020318) through edgeR. Ran the analysis using the Trinity differential expression pipeline:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Gene Expression - C.bairdi Pairwise DEG Comparisons with 2019 RNAseq using Trinity-Salmon-EdgeR on Mox

2020

Miscellaneous

Apr 22, 2020

Per a Slack request, Steven asked me to take the Genewize RNAseq data (received 2020318) through edgeR. Ran the analysis using the Trinity differential expression pipeline:

<<<<<<< HEAD

Apr 22, 2020

I previously annotated reads and converted them to the MEGAN6 format RMA6 on 20200414.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNAseq Reads Extractions - C.bairdi Taxonomic Reads Extractions with MEGAN6 on swoose

2020

Miscellaneous

Apr 19, 2020

I previously annotated reads and converted them to the MEGAN6 format RMA6 on 20200414.

<<<<<<< HEAD

Apr 19, 2020

Per this GitHub Issue, Grace and Steven asked if I could help by generating a transcript abundance file for Grace to use with EdgeR. To do so, I used Salmon for…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcript Abundance - C.bairdi Alignment-free with Salmon on Mox for Grace

2020

Miscellaneous

Per this GitHub Issue, Grace and Steven asked if I could help by generating a transcript abundance file for Grace to use with EdgeR. To do so, I used Salmon for…

<<<<<<< HEAD

Since we received the last of our RNAseq data for this project on 20200413, I submitted all of it to the NCBI Sequencing Read Archive (SRA). Data was released today and all…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

SRA Submission - C.bairdi RNAseq Data

2020

Miscellaneous

Since we received the last of our RNAseq data for this project on 20200413, I submitted all of it to the NCBI Sequencing Read Archive (SRA). Data was released today and all…

<<<<<<< HEAD

After receiving our RNAseq data from Genewiz earlier today, needed to trim and check trimmed reads with FastQC.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

TrimmingFastQCMultiQC—C.bairdi-RNAseq-FastQ-with-fastp-on-Mox

2020

Miscellaneous

After receiving our RNAseq data from Genewiz earlier today, needed to trim and check trimmed reads with FastQC.

<<<<<<< HEAD

After receiving/trimming the latest round of C.bairdi RNAseq data on 20200413, need to get the data ready to perform taxonomic selection of sequencing reads. To do this, I…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Taxonomic Assignments - C.bairdi RNAseq Using DIAMOND BLASTx on Mox and MEGAN6 Meganizer on swoose

2020

Miscellaneous

After receiving/trimming the latest round of C.bairdi RNAseq data on 20200413, need to get the data ready to perform taxonomic selection of sequencing reads. To do this, I…

<<<<<<< HEAD

Yesterday, we received the last of the RNAseq data for the C.bairdi crab project from NWGSC. FastQC, followed by MultiQC was run on the raw FastQ reads on my computer…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

FastQC-MultiQC - C.bairdi Raw RNAseq from NWGSC

2020

Miscellaneous

Yesterday, we received the last of the RNAseq data for the C.bairdi crab project from NWGSC. FastQC, followed by MultiQC was run on the raw FastQ reads on my computer…

<<<<<<< HEAD

After using MEGAN6 to extract Arthropoda and Alveolata reads from our RNAseq data on 20200330, I had then extracted taxonomic-specific reads and aggregated each into basic…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Wrangling - Arthropoda and Alveolata Day and Treatment Taxonomic RNAseq FastQ Extractions

2020

Miscellaneous

After using MEGAN6 to extract Arthropoda and Alveolata reads from our RNAseq data on 20200330, I had then extracted taxonomic-specific reads and aggregated each into basic…

<<<<<<< HEAD

Received the C.bairdi RNAseq data from UW NWGSC that Grace submitted on 20200131. Below is a table of NWGSC sample name and corresponding labels that Grace provided. The 0/1…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Received - C.bairdi RNAseq from NWGSC

2020

Data Received

Received the C.bairdi RNAseq data from UW NWGSC that Grace submitted on 20200131. Below is a table of NWGSC sample name and corresponding labels that Grace provided. The 0/1…

<<<<<<< HEAD

After performing de novo assembly on our Tanner crab MEGAN6 taxonomic-specific RNAseq data on 20200330 and performing BLASTx annotation on 20200408, I continued the…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Annotation - Trinotate C.bairdi MEGAN6 Taxonomic-specific Trinity Assembly on Mox

2020

Miscellaneous

Apr 9, 2020

After performing de novo assembly on our Tanner crab MEGAN6 taxonomic-specific RNAseq data on 20200330 and performing BLASTx annotation on 20200408, I continued the…

<<<<<<< HEAD

Apr 9, 2020

As part of annotating the most recent transcriptome assembly from the MEGAN6 Arthropoda taxonomic-specific reads, I need to run DIAMOND BLASTx to use with Trinotate.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Annotation - C.bairdi MEGAN Trinity Assembly Using DIAMOND BLASTx on Mox

2020

Miscellaneous

As part of annotating the most recent transcriptome assembly from the MEGAN6 Arthropoda taxonomic-specific reads, I need to run DIAMOND BLASTx to use with Trinotate.

<<<<<<< HEAD

After performing de novo assembly on our Hematodinium MEGAN6 taxonomic-specific RNAseq data on 20200330 and performing BLASTx annotation on 20200331, I continued the…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Annotation - Trinotate Hematodinium MEGAN6 Taxonomic-specific Trinity Assembly on Mox

2020

Miscellaneous

After performing de novo assembly on our Hematodinium MEGAN6 taxonomic-specific RNAseq data on 20200330 and performing BLASTx annotation on 20200331, I continued the…

<<<<<<< HEAD

Ran Trinity to de novo assembly on the the Alveolata MEGAN6 taxonomic-specific RNAseq data on 20120330 and now will begin annotating the transcriptome using TransDecoder on…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transdecoder - Hematodinium MEGAN6 Taxonomic-Specific Reads Assembly from 20200330

2020

Miscellaneous

Ran Trinity to de novo assembly on the the Alveolata MEGAN6 taxonomic-specific RNAseq data on 20120330 and now will begin annotating the transcriptome using TransDecoder on…

<<<<<<< HEAD

Ran Trinity to de novo assembly on the the Arthropoda MEGAN6 taxonomic-specific RNAseq data on 20120330 and now will begin annotating the transcriptome using TransDecoder on…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transdecoder - C.bairdi MEGAN6 Taxonomic-Specific Reads Assembly from 20200330

2020

Miscellaneous

Ran Trinity to de novo assembly on the the Arthropoda MEGAN6 taxonomic-specific RNAseq data on 20120330 and now will begin annotating the transcriptome using TransDecoder on…

<<<<<<< HEAD

I previously created a C.bairdi de novo transcriptome assembly with Trinity from the MEGAN6 taxonomic-specific reads for Arthropoda on 20200330 and decided to assess its…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Assessment - BUSCO Metazoa on C.bairdi MEGAN Transcriptome

2020

Miscellaneous

I previously created a C.bairdi de novo transcriptome assembly with Trinity from the MEGAN6 taxonomic-specific reads for Arthropoda on 20200330 and decided to assess its…

<<<<<<< HEAD

As part of annotating the most recent transcriptome assembly from the MEGAN6 Hematodinium taxonomic-specific reads, I need to run DIAMOND BLASTx to use with Trinotate.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Annotation - Hematodinium MEGAN Trinity Assembly Using DIAMOND BLASTx on Mox

2020

Miscellaneous

As part of annotating the most recent transcriptome assembly from the MEGAN6 Hematodinium taxonomic-specific reads, I need to run DIAMOND BLASTx to use with Trinotate.

<<<<<<< HEAD

I previously created a C.bairdi de novo transcriptome assembly with Trinity from the MEGAN6 taxonomic-specific reads for Alveolata on 20200331 and decided to assess its…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Assessment - BUSCO Metazoa on Hematodinium MEGAN Transcriptome

2020

Miscellaneous

I previously created a C.bairdi de novo transcriptome assembly with Trinity from the MEGAN6 taxonomic-specific reads for Alveolata on 20200331 and decided to assess its…

<<<<<<< HEAD

Ran a de novo assembly using the extracted reads classified under Alveolata from:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Assembly - Hematodinium with MEGAN6 Taxonomy-specific Reads with Trinity on Mox

2020

Miscellaneous

Ran a de novo assembly using the extracted reads classified under Alveolata from:

<<<<<<< HEAD

Ran a de novo assembly using the extracted reads classified under Arthropoda from:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Assembly - C.bairdi with MEGAN6 Taxonomy-specific Reads with Trinity on Mox

2020

Miscellaneous

Ran a de novo assembly using the extracted reads classified under Arthropoda from:

<<<<<<< HEAD

I previously annotated reads and converted them to the MEGAN6 format RMA6 on 20200318.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNAseq Reads Extractions - C.bairdi Taxonomic Reads Extractions with MEGAN6 on swoose

2020

Miscellaneous

I previously annotated reads and converted them to the MEGAN6 format RMA6 on 20200318.

<<<<<<< HEAD

After receiving/trimming the latest round of C.bairdi RNAseq data on 20200318, need to get the data ready to perform taxonomic selection of sequencing reads. To do this, I…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Annotation - C.bairdi Using DIAMOND BLASTx on Mox and MEGAN6 Meganizer on swoose

2020

Tanner Crab RNAseq

After receiving/trimming the latest round of C.bairdi RNAseq data on 20200318, need to get the data ready to perform taxonomic selection of sequencing reads. To do this, I…

<<<<<<< HEAD

After receiving our RNAseq data from Genewiz earlier today, needed to run FastQC, trim, check trimmed reads with FastQC.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Trimming/FastQC/MultiQC - C.bairdi RNAseq FastQ with fastp on Mox

2020

Tanner Crab RNAseq

After receiving our RNAseq data from Genewiz earlier today, needed to run FastQC, trim, check trimmed reads with FastQC.

<<<<<<< HEAD

We received the RNAseq data from the RNA that was sent out by Grace on 20200212.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Received - C.bairdi RNAseq Data from Genewiz

2020

Data Received

Tanner Crab RNAseq

We received the RNAseq data from the RNA that was sent out by Grace on 20200212.

<<<<<<< HEAD

Isolated DNA from 22 samples (see Qubit spreadsheet in “Results” below for sample IDs) using the Quick DNA/RNA Microprep Kit (ZymoResearch; PDF) according to the…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Isolation and Quantification - C.bairdi Hemocyte Pellets in RNAlater

2020

Miscellaneous

Isolated DNA from 22 samples (see Qubit spreadsheet in “Results” below for sample IDs) using the Quick DNA/RNA Microprep Kit (ZymoResearch; PDF) according to the…

<<<<<<< HEAD

After getting high quality gDNA from Hematodinium-infected C.bairdi hemolymph on 2020210 we decided to run some of the sample on the NanoPore MinION, since the flowcells…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

NanoPore Sequencing - C.bairdi gDNA 6129_403_26

2020

Miscellaneous

After getting high quality gDNA from Hematodinium-infected C.bairdi hemolymph on 2020210 we decided to run some of the sample on the NanoPore MinION, since the flowcells…

<<<<<<< HEAD

Previuosly checked existing crab RNA for residual gDNA on 20200226 and identified samples with yields that were likely too low, as well as samples with residual gDNA. For…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - C.bairdi RNA Check for Residual gDNA

2020

Tanner Crab RNAseq

Mar 10, 2020

Previuosly checked existing crab RNA for residual gDNA on 20200226 and identified samples with yields that were likely too low, as well as samples with residual gDNA. For…

<<<<<<< HEAD

Mar 10, 2020

Steven asked me to trim a set of FastQ files, provided by Hollie Putnam, in preparation for methylation analysis using Bismark. The analysis is part of a coral project…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Trimming/MultiQC - Methcompare Bisulfite FastQs with fastp on Mox

2020

Miscellaneous

Steven asked me to trim a set of FastQ files, provided by Hollie Putnam, in preparation for methylation analysis using Bismark. The analysis is part of a coral project…

<<<<<<< HEAD

Based on qPCR results testing for residual gDNA from 20200225, a set of 24 samples were identified that required DNase treatment and/or additional RNA. I opted to just…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation and Quantification - C.bairdi RNA from Hemolymph Pellets in RNAlater

2020

Tanner Crab RNAseq

Based on qPCR results testing for residual gDNA from 20200225, a set of 24 samples were identified that required DNase treatment and/or additional RNA. I opted to just…

<<<<<<< HEAD

I finally had some time to tackle this GitHub Issue and create a canonical genes FastA file using the MAKER IDs, instead of the original contig IDs from our Olympia oyster…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Wrangling - Create Canonical Olurida_v081 Genes FastA

2020

Miscellaneous

Feb 28, 2020

I finally had some time to tackle this GitHub Issue and create a canonical genes FastA file using the MAKER IDs, instead of the original contig IDs from our Olympia oyster…

<<<<<<< HEAD

Feb 28, 2020

After deciding on a primer set to use for gDNA detection on 20200225, went ahead and ran a qPCR on most of the RNA samples described in Grace’s Google Sheet. Some samples…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - C.bairdi RNA Check for Residual gDNA

2020

Tanner Crab RNAseq

Feb 26, 2020

After deciding on a primer set to use for gDNA detection on 20200225, went ahead and ran a qPCR on most of the RNA samples described in Grace’s Google Sheet. Some samples…

<<<<<<< HEAD

Feb 26, 2020

We received the primers I ordered on 20200220 and now need to test them to see if they detect gDNA. If yes, then they’re good candidates to assess the presence of residual…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - C.bairdi Primer Tests on gDNA

2020

Tanner Crab RNAseq

Feb 25, 2020

We received the primers I ordered on 20200220 and now need to test them to see if they detect gDNA. If yes, then they’re good candidates to assess the presence of residual…

<<<<<<< HEAD

Feb 25, 2020

Getting ready to run some qPCRs and first we need to confirm that our RNA is actually DNA-free. Before we can do that, we need some primers to use, so I decided to…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Primer Design - C.bairdi Primers for Checking RNA for Residual gDNA

2020

Tanner Crab RNAseq

Feb 20, 2020

Getting ready to run some qPCRs and first we need to confirm that our RNA is actually DNA-free. Before we can do that, we need some primers to use, so I decided to…

<<<<<<< HEAD

Feb 20, 2020

Isolated DNA from three samples (see Qubit spreadsheet in “Results” below for sample IDs) using the Quick DNA/RNA Microprep Kit (ZymoResearch; PDF) according to the…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Isolation & Quantification - C.bairdi RNA from Samples 6212_132_9 6212_334_12 6212_485_26

2020

Tanner Crab RNAseq

Isolated DNA from three samples (see Qubit spreadsheet in “Results” below for sample IDs) using the Quick DNA/RNA Microprep Kit (ZymoResearch; PDF) according to the…

<<<<<<< HEAD

We are supposed to get RNA sent out for sequencing today, but it turns out that a few of the designated samples have insufficient RNA in them. So, I’m going to attempt to…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation & Quantification - C.bairdi RNA from Samples 6212_132_9 6212_334_12 6212_485_26

2020

Tanner Crab RNAseq

We are supposed to get RNA sent out for sequencing today, but it turns out that a few of the designated samples have insufficient RNA in them. So, I’m going to attempt to…

<<<<<<< HEAD

Since I was isolating gDNA from C.bairdi 6129_403_26 hemolymph, I figured I might as well co-isolate RNA since I was using the Quick DNA/RNA Microprep Plus Kit (ZymoResearch).

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation & Quantification - C.bairdi RNA from Sample 6129_403_26

2020

Tanner Crab RNAseq

Since I was isolating gDNA from C.bairdi 6129_403_26 hemolymph, I figured I might as well co-isolate RNA since I was using the Quick DNA/RNA Microprep Plus Kit (ZymoResearch).

<<<<<<< HEAD

Earlier today I isolated gDNA from C.bairi 6129_403_26 hemolymph pellets and recovered decently intact gDNA that could be used for sequencing. However, I still need more…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Isolation & Quantification - Additional C.bairdi gDNA from Sample 6129_403_26

2020

Miscellaneous

Earlier today I isolated gDNA from C.bairi 6129_403_26 hemolymph pellets and recovered decently intact gDNA that could be used for sequencing. However, I still need more…

<<<<<<< HEAD

In order to do some genome sequencing on C.bairid and Hematodinium, we need hihg molecular weight gDNA. I attempted this twice before, using two different methods (Quick…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Isolation, Quantification, and Gel - C.bairdi gDNA Sample 6129_403_26

2020

Miscellaneous

In order to do some genome sequencing on C.bairid and Hematodinium, we need hihg molecular weight gDNA. I attempted this twice before, using two different methods (Quick…

<<<<<<< HEAD

I previously created a Hematodinium de novo transcriptome assembly with Trinity from the MEGAN6 taxonomic-specific reads for Alveolata on 20200122 and decided to assess its…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Assessment - BUSCO Metazoa on Hematodinium MEGAN Transcriptome

2020

Tanner Crab RNAseq

I previously created a Hematodinium de novo transcriptome assembly with Trinity from the MEGAN6 taxonomic-specific reads for Alveolata on 20200122 and decided to assess its…

<<<<<<< HEAD

I previously created a C.bairdi de novo transcriptome assembly with Trinity from the MEGAN6 taxonomic-specific reads for Arthropoda on 20200122 and decided to assess its…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Assessment - BUSCO Metazoa on C.bairdi MEGAN Transcriptome

2020

Tanner Crab RNAseq

I previously created a C.bairdi de novo transcriptome assembly with Trinity from the MEGAN6 taxonomic-specific reads for Arthropoda on 20200122 and decided to assess its…

<<<<<<< HEAD

After completing annotation of the Hematodinium MEGAN6 taxonomic-specific Trinity assembly using Trinotate on 20200126, I performed differential gene expression analysis and…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Gene Expression - Hematodinium MEGAN6 with Trinity and EdgeR

2020

Miscellaneous

After completing annotation of the Hematodinium MEGAN6 taxonomic-specific Trinity assembly using Trinotate on 20200126, I performed differential gene expression analysis and…

<<<<<<< HEAD

After completing annotation of the C.bairdi MEGAN6 taxonomic-specific Trinity assembly using Trinotate on 20200126, I performed differential gene expression analysis and…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Gene Expression - C.bairdi MEGAN6 with Trinity and EdgeR

2020

Tanner Crab RNAseq

After completing annotation of the C.bairdi MEGAN6 taxonomic-specific Trinity assembly using Trinotate on 20200126, I performed differential gene expression analysis and…

<<<<<<< HEAD

After using MEGAN6 to extract Arthropoda and Alveolata reads from our RNAseq data on 20200114, I had then extracted taxonomic-specific reads and aggregated each into basic…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Wrangling - Arthropoda and Alveolata Day and Treatment Taxonomic RNAseq FastQ Extractions

2020

Tanner Crab RNAseq

Jan 31, 2020

After using MEGAN6 to extract Arthropoda and Alveolata reads from our RNAseq data on 20200114, I had then extracted taxonomic-specific reads and aggregated each into basic…

<<<<<<< HEAD

Jan 31, 2020

Isolated DNA from 56 samples (see Qubit spreadsheet in “Results” below for sample IDs) using the Quick DNA/RNA Microprep Kit (ZymoResearch; PDF) according to the…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Isolation and Quantification - C.bairdi Hemocyte Pellets in RNAlater

2020

Miscellaneous

Jan 28, 2020

Isolated DNA from 56 samples (see Qubit spreadsheet in “Results” below for sample IDs) using the Quick DNA/RNA Microprep Kit (ZymoResearch; PDF) according to the…

<<<<<<< HEAD

Jan 28, 2020

After performing de novo assembly on our Hematodinium MEGAN6 taxonomic-specific RNAseq data on 20200122 and performing BLASTx annotation on 20200123, I continued the…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Annotation - Trinotate Hematodinium MEGAN6 Taxonomic-specific Trinity Assembly on Mox

2020

Tanner Crab RNAseq

After performing de novo assembly on our Hematodinium MEGAN6 taxonomic-specific RNAseq data on 20200122 and performing BLASTx annotation on 20200123, I continued the…

<<<<<<< HEAD

After performing de novo assembly on our Tanner crab MEGAN6 taxonomic-specific RNAseq data on 20200122 and performing BLASTx annotation on 20200123, I continued the…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Annotation - Trinotate C.bairdi MEGAN6 Taxonomic-specific Trinity Assembly on Mox

2020

Tanner Crab RNAseq

After performing de novo assembly on our Tanner crab MEGAN6 taxonomic-specific RNAseq data on 20200122 and performing BLASTx annotation on 20200123, I continued the…

<<<<<<< HEAD

Isolated RNA from the following hemolymph pellet samples:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation and Quantification - C.bairdi Hemocyte Pellets in RNAlater

2020

Tanner Crab RNAseq

Isolated RNA from the following hemolymph pellet samples:

<<<<<<< HEAD

Isolated RNA from the following hemolymph pellet samples:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation and Quantification - C.bairdi Hemocyte Pellets in RNAlater

2020

Tanner Crab RNAseq

Jan 24, 2020

Isolated RNA from the following hemolymph pellet samples:

<<<<<<< HEAD

Jan 24, 2020

Ran Trinity to de novo assembly on the the C.bairdi MEGAN6 taxonomic-specific RNAseq data on 201200122 and now will begin annotating the transcriptome using TransDecoder on…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transdecoder - Hematodinium MEGAN6 Taxonomic-Specific Reads Assembly from 20200122

2020

Miscellaneous

Ran Trinity to de novo assembly on the the C.bairdi MEGAN6 taxonomic-specific RNAseq data on 201200122 and now will begin annotating the transcriptome using TransDecoder on…

<<<<<<< HEAD

Ran Trinity to de novo assembly on the the Hematodinium MEGAN6 taxonomic-specific RNAseq data on 201200122 and now will begin annotating the transcriptome using TransDecoder…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transdecoder - C.bairdi MEGAN6 Taxonomic-Specific Reads Assembly from 20200122

2020

Tanner Crab RNAseq

Ran Trinity to de novo assembly on the the Hematodinium MEGAN6 taxonomic-specific RNAseq data on 201200122 and now will begin annotating the transcriptome using TransDecoder…

<<<<<<< HEAD

As part of annotating the transcriptome assembly from the MEGAN6 Hematodinium taxonomic-specific reads, I need to run DIAMOND BLASTx to use with Trinotate.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Annotation - Hematodinium MEGAN Trinity Assembly Using DIAMOND BLASTx on Mox

2020

Miscellaneous

As part of annotating the transcriptome assembly from the MEGAN6 Hematodinium taxonomic-specific reads, I need to run DIAMOND BLASTx to use with Trinotate.

<<<<<<< HEAD

As part of annotating the transcriptome assembly from the MEGAN6 C.bairdi taxonomic-specific reads, I need to run DIAMOND BLASTx to use with Trinotate.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Annotation - C.bairdi MEGAN Trinity Assembly Using DIAMOND BLASTx on Mox

2020

Tanner Crab RNAseq

As part of annotating the transcriptome assembly from the MEGAN6 C.bairdi taxonomic-specific reads, I need to run DIAMOND BLASTx to use with Trinotate.

<<<<<<< HEAD

After the failure to obtain RNA from any C.bairdi hemocytes pellets (out of 24 samples processed) on 20200117, I decided to isolate RNA from just a subset of that group to…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation and Quantification - C.bairdi Hemocyte Pellets in RNAlater Troubleshooting

2020

Tanner Crab RNAseq

After the failure to obtain RNA from any C.bairdi hemocytes pellets (out of 24 samples processed) on 20200117, I decided to isolate RNA from just a subset of that group to…

<<<<<<< HEAD

Earlier today, I isolated gDNA from C.bairdi 20102558-2729 ethanol-preserved muscle tissue using the Quick DNA/RNA MicroPrep Plus Kit (ZymoResearch) and prepared the tissue…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Quality Assessment - Agarose Gel for C.bairdi 20102558-2729 gDNA from 20200122

2020

Miscellaneous

Earlier today, I isolated gDNA from C.bairdi 20102558-2729 ethanol-preserved muscle tissue using the Quick DNA/RNA MicroPrep Plus Kit (ZymoResearch) and prepared the tissue…

<<<<<<< HEAD

After using MEGAN6 to extract Arthropoda and Alveolata reads from our RNAseq data on 20200114 (for reference, these include RNAseq data using a newly established…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Wrangling - Arthropoda and Alveolata Taxonomic RNAseq FastQ Extractions

2020

Tanner Crab RNAseq

After using MEGAN6 to extract Arthropoda and Alveolata reads from our RNAseq data on 20200114 (for reference, these include RNAseq data using a newly established…

<<<<<<< HEAD

Previously, I isolated gDNA from a C.bairdi EtOH-preserved muscle sample (20102558-2729) on 20200108 using the E.Z.N.A. Mollusc DNA Kit (Omega). Although the yields were…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Isolation - C.bairdi 20102558-2729 EtOH-preserved Tissue via Three Variations Using Quick DNA-RNA MicroPrep Kit

2020

Miscellaneous

Previously, I isolated gDNA from a C.bairdi EtOH-preserved muscle sample (20102558-2729) on 20200108 using the E.Z.N.A. Mollusc DNA Kit (Omega). Although the yields were…

<<<<<<< HEAD

Ran a de novo assembly using the extracted reads classified under Alveolata from 20200122 The assembly was performed with Trinity on Mox.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Assembly - Hematodinium with MEGAN6 Taxonomy-specific Reads with Trinity on Mox

2020

Miscellaneous

Ran a de novo assembly using the extracted reads classified under Alveolata from 20200122 The assembly was performed with Trinity on Mox.

<<<<<<< HEAD

Ran a de novo assembly using the extracted reads classified under Arthropoda from 20200122 (for reference, these include RNAseq data using a newly established “shorthand”…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Assembly - C.bairdi with MEGAN6 Taxonomy-specific Reads with Trinity on Mox

2020

Tanner Crab RNAseq

Ran a de novo assembly using the extracted reads classified under Arthropoda from 20200122 (for reference, these include RNAseq data using a newly established “shorthand”…

<<<<<<< HEAD

Isolated DNA from the following 23 samples:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Isolation and Quantification - C.bairdi Hemolymph Pellets in RNAlater

2020

Miscellaneous

Isolated DNA from the following 23 samples:

<<<<<<< HEAD

TL;DR - Recovered absolutely no RNA from any sample! However, I did recover DNA from each sample.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation and Quantification - C.bairdi Hemolymph Pellets in RNAlater

2020

Tanner Crab RNAseq

TL;DR - Recovered absolutely no RNA from any sample! However, I did recover DNA from each sample.

<<<<<<< HEAD

I previously ran BLASTx and “meganized” the output DAA files on 20200103 (for reference, these include RNAseq data using a newly established “shorthand”: 2018, 2019) and now…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNAseq Reads Extractions - C.bairdi Taxonomic Reads Extractions with MEGAN6 on swoose

2020

Tanner Crab RNAseq

Jan 14, 2020

I previously ran BLASTx and “meganized” the output DAA files on 20200103 (for reference, these include RNAseq data using a newly established “shorthand”: 2018, 2019) and now…

<<<<<<< HEAD

Jan 14, 2020

Replaced the batteries on one of the APC uninterruptable power supplies (UPS) on our local server cabinet.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Lab Maintenance - Cluster UPS Battery Replacement

2020

Miscellaneous

Jan 10, 2020

Replaced the batteries on one of the APC uninterruptable power supplies (UPS) on our local server cabinet.

<<<<<<< HEAD

Jan 10, 2020

I performed the initial Lambda sequencing test on 20200107 and everything went smoothly, so I’m ready to give the NanoPore (ONT) MinION a run with an actual sample!

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

NanoPore Sequencing - C.bairdi gDNA Sample 20102558-2729

2020

Miscellaneous

I performed the initial Lambda sequencing test on 20200107 and everything went smoothly, so I’m ready to give the NanoPore (ONT) MinION a run with an actual sample!

<<<<<<< HEAD

I isolated C.bairdi gDNA yesterday (20200108) and now want to get an idea if it’s any good (i.e. no contaminants, high molecule weight).

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Quality Assessment - Agarose Gel and NanoDrop on C.bairdi gDNA

2020

Miscellaneous

I isolated C.bairdi gDNA yesterday (20200108) and now want to get an idea if it’s any good (i.e. no contaminants, high molecule weight).

<<<<<<< HEAD

I isolated gDNA from ethanol-preserved C.bairdi muscle tissue from sample 20102558-2729 (SPNO-ReferenceNO). This sample was chosen as it had 0 in the SMEAR_result and BCS_PCR…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Isolation and Quantification - C.bairdi gDNA from EtOH Preserved Tissue

2020

Miscellaneous

Jan 8, 2020

I isolated gDNA from ethanol-preserved C.bairdi muscle tissue from sample 20102558-2729 (SPNO-ReferenceNO). This sample was chosen as it had 0 in the SMEAR_result and BCS_PCR…

<<<<<<< HEAD

Jan 8, 2020

We recently acquired a NanoPore MinION sequencer, FLO-MIN106 flow cell and the Rapid Sequencing Kit (SQK-RAD004). The NanoPore website provides a pretty thorough an…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

NanoPore Sequencing - Initial NanoPore MinION Lambda Sequencing Test

2020

Miscellaneous

Jan 7, 2020

We recently acquired a NanoPore MinION sequencer, FLO-MIN106 flow cell and the Rapid Sequencing Kit (SQK-RAD004). The NanoPore website provides a pretty thorough an…

<<<<<<< HEAD

Jan 7, 2020

Although I previously annotated our C.bairdi transcriptome from 20191218, I realized that the assembly and annotations were combine infected/uninfected samples, possibly…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Annotation - C.bairdi Using DIAMOND BLASTx on Mox and MEGAN6 Meganizer

2020

Tanner Crab RNAseq

Jan 3, 2020

Although I previously annotated our C.bairdi transcriptome from 20191218, I realized that the assembly and annotations were combine infected/uninfected samples, possibly…

<<<<<<< HEAD

Jan 3, 2020

Created aliquots of RNA Pico Ladder received on 20191101, per the manufacturer’s instructions. Created single-use aliquots of 1.5uL and stored at -80^oC:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Reagent Prep - RNA Pico Ladder Aliquoting and Testing

2020

Reagent Prep

Jan 2, 2020

Created aliquots of RNA Pico Ladder received on 20191101, per the manufacturer’s instructions. Created single-use aliquots of 1.5uL and stored at -80^oC:

<<<<<<< HEAD

Jan 2, 2020

After performing de novo assembly on our Tanner crab RNAseq data on 20191218 and performing BLASTx annotation on 20191224, I continued the annotation process by running Trino…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Annotation - C.bairdi Trinity Assembly Trinotate on Mox

2019

Tanner Crab RNAseq

Dec 25, 2019

After performing de novo assembly on our Tanner crab RNAseq data on 20191218 and performing BLASTx annotation on 20191224, I continued the annotation process by running Trino…

<<<<<<< HEAD

Dec 25, 2019

In preparation for complete transcriptome annotation of the C.bairdi de novo assembly fro 20191218, I needed to run BLASTx. The assembly was BLASTed against the SwissProt…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Annotation - C.bairdi Trinity Assembly BLASTx on Mox

2019

Tanner Crab RNAseq

Dec 24, 2019

In preparation for complete transcriptome annotation of the C.bairdi de novo assembly fro 20191218, I needed to run BLASTx. The assembly was BLASTed against the SwissProt…

<<<<<<< HEAD

Dec 24, 2019

Ran Trinity to de novo assemble the C.bairdi RNAseq data we had on 20191218 and now will begin annotating the transcriptome using TransDecoder on Mox.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transdecoder - C.bairdi De Novo Transcriptome from 20191218 on Mox

2019

Tanner Crab RNAseq

Dec 20, 2019

Ran Trinity to de novo assemble the C.bairdi RNAseq data we had on 20191218 and now will begin annotating the transcriptome using TransDecoder on Mox.

<<<<<<< HEAD

Dec 20, 2019

Earlier today, I trimmed our existing C.bairdi RNAseq data, as part of producing generating a transcriptome (per this GitHub issue). After trimming, I performed a de novo ass…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Assembly - C.bairdi Trimmed RNAseq Using Trinity on Mox

2019

Tanner Crab RNAseq

Earlier today, I trimmed our existing C.bairdi RNAseq data, as part of producing generating a transcriptome (per this GitHub issue). After trimming, I performed a de novo ass…

<<<<<<< HEAD

Grace/Steven asked me to generate a de novo transcriptome assembly of our current C.bairdi RNAseq data in this GitHub issue. As part of that, I needed to quality trim the…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Trimming/FastQC/MultiQC - C.bairdi RNAseq FastQ with fastp on Mox

2019

Tanner Crab RNAseq

Grace/Steven asked me to generate a de novo transcriptome assembly of our current C.bairdi RNAseq data in this GitHub issue. As part of that, I needed to quality trim the…

<<<<<<< HEAD

After a meeting last week, we realized we needed to update the paper-oly-mbdbs-gen GitHub repo with the most current versions of feature files we had.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Wrangling - Olurida_v081 UTR GFFs and Intergenic, Intron BED files

2019

Miscellaneous

Dec 14, 2019

After a meeting last week, we realized we needed to update the paper-oly-mbdbs-gen GitHub repo with the most current versions of feature files we had.

<<<<<<< HEAD

Dec 14, 2019

We received frozen Crassostrea gigas tissues from Maria Haws in Hawaii, as part of a pCO₂ experiment. Tissues include:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Samples Received - Pacific Oyster Tissues from Hawaii (Maria Haws) from High and Low pCO2

2019

Samples Received

Dec 10, 2019

We received frozen Crassostrea gigas tissues from Maria Haws in Hawaii, as part of a pCO₂ experiment. Tissues include:

<<<<<<< HEAD

Dec 10, 2019

In the final GFF from our GenSAS Pgenerosa_v074.a4 annotation, we noticed that there were no repeat motifs/sequences identified on Scaffold 01. The remaining scaffolds all…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Wrangling - Renaming, Splitting, and Feature Counts of Updated Pgenerosa_v074 GenSAS Merged GFF

2019

Geoduck Genome Sequencing

In the final GFF from our GenSAS Pgenerosa_v074.a4 annotation, we noticed that there were no repeat motifs/sequences identified on Scaffold 01. The remaining scaffolds all…

<<<<<<< HEAD

I ran this PCR a couple of times before and, embarrassingly, I had ordered/used the wrong primers.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

PCR - Crassostrea gigas and sikamea Mantle gDNA from Marinelli Shellfish Company

2019

Miscellaneous

I ran this PCR a couple of times before and, embarrassingly, I had ordered/used the wrong primers.

<<<<<<< HEAD

Pam Jensen (NOAA) brought by a variety of hemolymph and tissues stored in ethanol to use for DNA sequencing with the new MinION (Oxford Nanopore) to help aid our…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Samples Received - C.bairdi Hemolymph and Tissue in Ethanol from Pam Jensen

2019

Samples Received

Pam Jensen (NOAA) brought by a variety of hemolymph and tissues stored in ethanol to use for DNA sequencing with the new MinION (Oxford Nanopore) to help aid our…

<<<<<<< HEAD

Previously isolated RNA on 20191125 and made cDNA on 20191126 from some geoduck hemolymph and hemocyte samples that Shelly asked me to run qPCRs on.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Geoduck hemolymph and hemocyte cDNA with vitellogenin primers

2019

Miscellaneous

Previously isolated RNA on 20191125 and made cDNA on 20191126 from some geoduck hemolymph and hemocyte samples that Shelly asked me to run qPCRs on.

<<<<<<< HEAD

Performed reverse transcription on the DNased hemolymph and hemocyte RNA from yesterday.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Reverse Transcription - P.generosa DNased Hemolypmh and Hemocyte RNA from 20191125

2019

Miscellaneous

Nov 26, 2019

Performed reverse transcription on the DNased hemolymph and hemocyte RNA from yesterday.

<<<<<<< HEAD

Nov 26, 2019

Shelly asked me to isolate RNA and run some qPCRs on the following samples:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation and Quantification - Geoduck hemolymph and hemocyte samples

2019

Miscellaneous

Nov 25, 2019

Shelly asked me to isolate RNA and run some qPCRs on the following samples:

<<<<<<< HEAD

Nov 25, 2019

Since the results I obtained on my final attempt to get this to work failed, I decided to double-check the primer sequences.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

PCR - Crassostrea gigas and sikamea Mantle gDNA from Marinellie Shellfish Company - No Multiplex

2019

Miscellaneous

Since the results I obtained on my final attempt to get this to work failed, I decided to double-check the primer sequences.

<<<<<<< HEAD

Since the results I obtained on my final attempt to get this to work failed, I decided to double-check the primer sequences.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

PCR - Crassostrea gigas and sikamea Mantle gDNA from Marinelli Shellfish Company

2019

Miscellaneous

Since the results I obtained on my final attempt to get this to work failed, I decided to double-check the primer sequences.

<<<<<<< HEAD

After a meeting today, Steven and Hollie realized that the Bismark coverage files were still using the old scaffold names, stemming from the Pgenerosa_v074 naming. I’d previo…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Wrangling - Rename Pgenerosa_v074 Bismark Coverage Files Scaffold Names

2019

Geoduck Genome Sequencing

Nov 20, 2019

After a meeting today, Steven and Hollie realized that the Bismark coverage files were still using the old scaffold names, stemming from the Pgenerosa_v074 naming. I’d previo…

<<<<<<< HEAD

Nov 20, 2019

Since the results I obtained on my final attempt to get this to work failed, I decided to double-check the primer sequences.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

PCR - Crassostrea gigas and sikamea Mantle gDNA from Marinelli Shellfish Company

2019

Miscellaneous

Since the results I obtained on my final attempt to get this to work failed, I decided to double-check the primer sequences.

<<<<<<< HEAD

Isolated DNA from the C.gigas and C.sikamea samples we received from Marinelli Shellfish Company on 20191030 using DNAzol.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Isolation and Quantification - Crassostrea gigas and Crassostrea sikamea Mantle Tissue from Marinelli Shellfish Company

2019

Miscellaneous

Isolated DNA from the C.gigas and C.sikamea samples we received from Marinelli Shellfish Company on 20191030 using DNAzol.

<<<<<<< HEAD

Although I’d previously generated some feature stats for this genome annotation (see 20191029), we decided we wanted to get some additional info, similar to that of Table 1 i…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Wrangling - Additional Features Stats for Panopea-generosa-v1.0

2019

Geoduck Genome Sequencing

Nov 6, 2019

Although I’d previously generated some feature stats for this genome annotation (see 20191029), we decided we wanted to get some additional info, similar to that of Table 1 i…

<<<<<<< HEAD

Nov 6, 2019

Continuing to organizing files for a manuscript dealing with the geoduck genome assembly/annotation we’ve done, we decided to rename the files as well as rename the…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Wrangling - Rename Pgenerosa_v074 Files and Scaffolds

2019

Geoduck Genome Sequencing

Nov 5, 2019

Continuing to organizing files for a manuscript dealing with the geoduck genome assembly/annotation we’ve done, we decided to rename the files as well as rename the…

<<<<<<< HEAD

Nov 5, 2019

We’re in the process of organizing files for a manuscript dealing with the geoduck genome assembly/annotation we’ve done. As part of that, we need the Stringtie BAM file…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Wrangling - Splitting BAM by Size for Upload to OSF

2019

Geoduck Genome Sequencing

Oct 31, 2019

We’re in the process of organizing files for a manuscript dealing with the geoduck genome assembly/annotation we’ve done. As part of that, we need the Stringtie BAM file…

<<<<<<< HEAD

Oct 31, 2019

Steven was recently contacted by Marinelli Shellfish Company to see if we could help them determine if some oysters they had were Crassostrea gigas (Pacific oyster) or Crasso…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Samples Received - Marinelli Shellfish Company C.gigas and C.sikamea Oysters

2019

Miscellaneous

Steven was recently contacted by Marinelli Shellfish Company to see if we could help them determine if some oysters they had were Crassostrea gigas (Pacific oyster) or Crasso…

<<<<<<< HEAD

Since generating an updated Pgenerosa_v074 annotation, we also needed updated intergenic and intron bed files to put in the OSF repository for this project.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Wrangling - Create Panopea-generosa-vv0.74.a4 Intron and Intergenic BED Files

2019

Geoduck Genome Sequencing

Since generating an updated Pgenerosa_v074 annotation, we also needed updated intergenic and intron bed files to put in the OSF repository for this project.

<<<<<<< HEAD

Due to a bug with GenSAS, the final GFF generated by their system to did not properly merge all of the repeats data properly. The repeats data below should be ignored! It…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genome Feature Counts - Panopea-generosa-vv0.74.a4

2019

Geoduck Genome Sequencing

Oct 29, 2019

Due to a bug with GenSAS, the final GFF generated by their system to did not properly merge all of the repeats data properly. The repeats data below should be ignored! It…

<<<<<<< HEAD

Oct 29, 2019

After receiving the rest of the crab data and concatenating it all together, I ran FastQC and MultiQC on the FastQ files.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

FastQC-MultiQC - C.bairdi RNAseq Day 12 26 Infected Uninfected

2019

Tanner Crab RNAseq

After receiving the rest of the crab data and concatenating it all together, I ran FastQC and MultiQC on the FastQ files.

<<<<<<< HEAD

Previously, we “received” this data, but it turns out it was incomplete (see 20191003).

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Received - C.bairdi RNAseq Day9-12-26 Infected-Uninfected

2019

Tanner Crab RNAseq

Data Received

Previously, we “received” this data, but it turns out it was incomplete (see 20191003).

<<<<<<< HEAD

Replaced the batteries on one of the APC uninterruptable power supplies (UPS) on our local server cabinet.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Lab Maintenance - Cluster UPS Battery Replacement

2019

Miscellaneous

Oct 22, 2019

Replaced the batteries on one of the APC uninterruptable power supplies (UPS) on our local server cabinet.

<<<<<<< HEAD

Oct 22, 2019

After running DIAMOND BLASTx and MEGANIZER on these samples on 20190925 to assess taxonomy info, I began the analyses/visualization of this data with MEGAN6.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Metagenomics Annotation - P.generosa Water Samples with MEGAN6

2019

Miscellaneous

Oct 14, 2019

After running DIAMOND BLASTx and MEGANIZER on these samples on 20190925 to assess taxonomy info, I began the analyses/visualization of this data with MEGAN6.

<<<<<<< HEAD

Oct 14, 2019

Finally received the RNAseq data back from NWGC that we submitted on 20190521!

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Received - C.bairdi RNAseq Day9-12-26 Infected-Uninfected

2019

Tanner Crab RNAseq

Oct 3, 2019

Finally received the RNAseq data back from NWGC that we submitted on 20190521!

<<<<<<< HEAD

Oct 3, 2019

I’d previously annotated our Pgenerosa_v074 with GenSAS, but did so using limited options as we were (and still are) in need of an annotated genome to use for methylation…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genome Annotation - Pgenerosa_v074 a4 Using GenSAS

2019

Geoduck Genome Sequencing

Sep 28, 2019

I’d previously annotated our Pgenerosa_v074 with GenSAS, but did so using limited options as we were (and still are) in need of an annotated genome to use for methylation…

<<<<<<< HEAD

Sep 28, 2019

We recently had a meeting with Emma and Brook about the progress of this metagenomics project and Brook suggested trying out MEGAN6 as user-friendly way to get these samples…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Metagenomics Annotation - P.generosa Water Samples Using DIAMOND BLASTx on Mox

2019

Miscellaneous

Sep 25, 2019

We recently had a meeting with Emma and Brook about the progress of this metagenomics project and Brook suggested trying out MEGAN6 as user-friendly way to get these samples…

<<<<<<< HEAD

Sep 25, 2019

Steven noticed that the M-Bias plots generated by Bismark from these files was a little wonky and asked that I try trimming them a bit more. The files were originally…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Trimming/FastQC/MultiQC - P.generosa EPI FastQs with FASTP on Mox

2019

Miscellaneous

Sep 23, 2019

Steven noticed that the M-Bias plots generated by Bismark from these files was a little wonky and asked that I try trimming them a bit more. The files were originally…

<<<<<<< HEAD

Sep 23, 2019

Submitted sequencing data (52 samples; see table below) from Hollie’s BS-seq project looking at differences in DNA methylation between juvenile geoduck exposed to different…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

SRA Submission - Hollie’s Juvenile OA BS-seq Data

2019

SRA Submissions

Sep 18, 2019

Submitted sequencing data (52 samples; see table below) from Hollie’s BS-seq project looking at differences in DNA methylation between juvenile geoduck exposed to different…

<<<<<<< HEAD

Sep 18, 2019

Needed to pull some numbers on repeats in our Pgenerosa_v074.a3 GenSAS annotation (from 20190710) for the manuscript we’re putting together.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Wrangling - Pgenerosa_v074.a3 Annotation Genome Repeats Compostion

2019

Geoduck Genome Sequencing

Sep 5, 2019

Needed to pull some numbers on repeats in our Pgenerosa_v074.a3 GenSAS annotation (from 20190710) for the manuscript we’re putting together.

<<<<<<< HEAD

Sep 5, 2019

The GenSAS Pgenerosa_v074 annotation from 20190710 (referred to as: Panopea-generosa-vv0.74.a3) recently completed (after nearly a month of running).

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Wrangling - Pgenerosa_v074.a3 Annotation Genome Feature Sequence Lengths

2019

Geoduck Genome Sequencing

Sep 4, 2019

The GenSAS Pgenerosa_v074 annotation from 20190710 (referred to as: Panopea-generosa-vv0.74.a3) recently completed (after nearly a month of running).

<<<<<<< HEAD

Sep 4, 2019

In preparation for a paper we’re writing, we needed some summary stats on the various genome assembly feature sequences. I determined the max/min, mean, and median sequence…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Wrangling - Panopea generosa Genome Feature Sequence Lengths

2019

Geoduck Genome Sequencing

Aug 26, 2019

In preparation for a paper we’re writing, we needed some summary stats on the various genome assembly feature sequences. I determined the max/min, mean, and median sequence…

<<<<<<< HEAD

Aug 26, 2019

Steven wanted me to create a CpG GFF for use in IGV visulations for continued Pgenerosa_v074 analysis. I did that by running the EMBOSS tool fuzznuc:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Wrangling - Create a CpG GFF from Pgenerosa_v074 using EMBOSS fuzznuc on Swoose

2019

Geoduck Genome Sequencing

Aug 21, 2019

Steven wanted me to create a CpG GFF for use in IGV visulations for continued Pgenerosa_v074 analysis. I did that by running the EMBOSS tool fuzznuc:

<<<<<<< HEAD

Aug 21, 2019

For reference, this annotation will be referred to as Pgenerosa_v074.1.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genome Annotation - Pgenerosa_v074 MAKER on Mox with Stringtie Transcripts GFF

2019

Geoduck Genome Sequencing

Aug 19, 2019

For reference, this annotation will be referred to as Pgenerosa_v074.1.

<<<<<<< HEAD

Aug 19, 2019

In continuing to further improve our geoduck genome annotation, I’m attempting to figure out why Scaffold 1 of our assembly doesn’t have any annotations. As part of that…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genome Comparison - Pgenerosa_v074 vs Pgenerosa_v070 with MUMmer Promer on Mox

2019

Miscellaneous

In continuing to further improve our geoduck genome annotation, I’m attempting to figure out why Scaffold 1 of our assembly doesn’t have any annotations. As part of that…

<<<<<<< HEAD

In continuing to further improve our geoduck genome annotation, I’m attempting to figure out why Scaffold 1 of our assembly doesn’t have any annotations. As part of that…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genome Comparison - Pgenerosa_v074 vs S.glomerata NCBI with MUMmer Promer on Mox

2019

Miscellaneous

In continuing to further improve our geoduck genome annotation, I’m attempting to figure out why Scaffold 1 of our assembly doesn’t have any annotations. As part of that…

<<<<<<< HEAD

In continuing to further improve our geoduck genome annotation, I’m attempting to figure out why Scaffold 1 of our assembly doesn’t have any annotations. As part of that…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genome Comparison - Pgenerosa_v074 vs M.yessoensis NCBI with MUMmer Promer on Mox

2019

Miscellaneous

In continuing to further improve our geoduck genome annotation, I’m attempting to figure out why Scaffold 1 of our assembly doesn’t have any annotations. As part of that…

<<<<<<< HEAD

In continuing to further improve our geoduck genome annotation, I’m attempting to figure out why Scaffold 1 of our assembly doesn’t have any annotations. As part of that…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genome Comparison - Pgenerosa_v074 vs H.sapiens NCBI with MUMmer Promer on Mox

2019

Miscellaneous

In continuing to further improve our geoduck genome annotation, I’m attempting to figure out why Scaffold 1 of our assembly doesn’t have any annotations. As part of that…

<<<<<<< HEAD

In continuing to further improve our geoduck genome annotation, I’m attempting to figure out why Scaffold 1 of our assembly doesn’t have any annotations. As part of that…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genome Comparison - Pgenerosa_v074 vs C.virginica NCBI with MUMmer Promer on Mox

2019

Miscellaneous

In continuing to further improve our geoduck genome annotation, I’m attempting to figure out why Scaffold 1 of our assembly doesn’t have any annotations. As part of that…

<<<<<<< HEAD

In continuing to further improve our geoduck genome annotation, I’m attempting to figure out why Scaffold 1 of our assembly doesn’t have any annotations. As part of that…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genome Comparison - Pgenerosa_v074 vs C.gigas NCBI with MUMmer Promer on Mox

2019

Miscellaneous

In continuing to further improve our geoduck genome annotation, I’m attempting to figure out why Scaffold 1 of our assembly doesn’t have any annotations. As part of that…

<<<<<<< HEAD

In continuing to further improve our geoduck genome annotation, I’m attempting to figure out why Scaffold 1 of our assembly doesn’t have any annotations. As part of that…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genome Comparison - Pgenerosa_v074 vs Pgenerosa_v070 with MUMmer on Mox

2019

Miscellaneous

In continuing to further improve our geoduck genome annotation, I’m attempting to figure out why Scaffold 1 of our assembly doesn’t have any annotations. As part of that…

<<<<<<< HEAD

In continuing to further improve our geoduck genome annotation, I’m attempting to figure out why Scaffold 1 of our assembly doesn’t have any annotations. As part of that…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genome Comparison - Pgenerosa_v074 vs Pgenerosa_v074 with MUMmer on Mox

2019

Miscellaneous

In continuing to further improve our geoduck genome annotation, I’m attempting to figure out why Scaffold 1 of our assembly doesn’t have any annotations. As part of that…

<<<<<<< HEAD

In continuing to further improve our geoduck genome annotation, I’m attempting to figure out why Scaffold 1 of our assembly doesn’t have any annotations. As part of that…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genome Comparison - Pgenerosa_v074 vs S.glomerata NCBI with MUMmer on Mox

2019

Miscellaneous

In continuing to further improve our geoduck genome annotation, I’m attempting to figure out why Scaffold 1 of our assembly doesn’t have any annotations. As part of that…

<<<<<<< HEAD

In continuing to further improve our geoduck genome annotation, I’m attempting to figure out why Scaffold 1 of our assembly doesn’t have any annotations. As part of that…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genome Comparison - Pgenerosa_v074 vs M.yessoensis NCBI with MUMmer on Mox

2019

Miscellaneous

In continuing to further improve our geoduck genome annotation, I’m attempting to figure out why Scaffold 1 of our assembly doesn’t have any annotations. As part of that…

<<<<<<< HEAD

In continuing to further improve our geoduck genome annotation, I’m attempting to figure out why Scaffold 1 of our assembly doesn’t have any annotations. As part of that…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genome Comparison - Pgenerosa_v074 vs H.sapiens NCBI with MUMmer on Mox

2019

Miscellaneous

<<<<<<< HEAD

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

In continuing to further improve our geoduck genome annotation, I’m attempting to figure out why Scaffold 1 of our assembly doesn’t have any annotations. As part of that…

<<<<<<< HEAD

In continuing to further improve our geoduck genome annotation, I’m attempting to figure out why Scaffold 1 of our assembly doesn’t have any annotations. As part of that…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genome Comparison - Pgenerosa_v074 vs C.gigas NCBI with MUMmer on Mox

2019

Miscellaneous

In continuing to further improve our geoduck genome annotation, I’m attempting to figure out why Scaffold 1 of our assembly doesn’t have any annotations. As part of that…

Genome Comparison - Pgenerosa_v074 vs C.virginica NCBI with MUMmer on Mox

2019

Miscellaneous

In continuing to further improve our geoduck genome annotation, I’m attempting to figure out why Scaffold 1 of our assembly doesn’t have any annotations. As part of that…

<<<<<<< HEAD

Continuing our various attempts at annotating our geoduck genome assemblies, I will be re-annotating our Pgenerosa_v070 (see Genome Resources GitHub wiki for deets) and…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RepeatMasker - Pgenerosa_v070 for Transposable Element ID on Roadrunner

2019

Geoduck Genome Sequencing

Continuing our various attempts at annotating our geoduck genome assemblies, I will be re-annotating our Pgenerosa_v070 (see Genome Resources GitHub wiki for deets) and…

<<<<<<< HEAD

Steven posted an issue on GitHub regarding splitting a FastA file into multiple sequences. Specifically, he wanted a single, large FastA sequence (~89Mbp) split into smaller…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Wrangling - FastA Splitting With faSplit

2019

Miscellaneous

Jul 31, 2019

Steven posted an issue on GitHub regarding splitting a FastA file into multiple sequences. Specifically, he wanted a single, large FastA sequence (~89Mbp) split into smaller…

<<<<<<< HEAD

Jul 31, 2019

In our continuing quest to wrangle the geoduck transcriptome assemblies we have, I was tasked with compiling assembly stats for our various assemblies. The table below…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Summary - P.generosa Transcriptome Assemblies Stats

2019

Miscellaneous

In our continuing quest to wrangle the geoduck transcriptome assemblies we have, I was tasked with compiling assembly stats for our various assemblies. The table below…

<<<<<<< HEAD

In continued attempts to get a grasp on the geoduck transcriptome size, I decided to “compress” our various assemblies by clustering similar transcripts in each assembly in…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Compression - P.generosa Transcriptome Assemblies Using CD-Hit-est on Mox

2019

Miscellaneous

In continued attempts to get a grasp on the geoduck transcriptome size, I decided to “compress” our various assemblies by clustering similar transcripts in each assembly in…

<<<<<<< HEAD

After annotating Pgenerosa_v070 and comparing feature counts, there was a drastic difference between the two genome versions. Additionally, both of those genomes ended up…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genome Annotation - Pgenerosa_v074 Transcript Isoform ID with Stringtie on Mox

2019

Geoduck Genome Sequencing

After annotating Pgenerosa_v070 and comparing feature counts, there was a drastic difference between the two genome versions. Additionally, both of those genomes ended up…

<<<<<<< HEAD

After annotating Pgenerosa_v074 and comparing feature counts, there was a drastic difference between the two genome versions. Additionally, both of those genomes ended up…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genome Annotation - Pgenerosa_v070 Transcript Isoform ID with Stringtie on Mox

2019

Geoduck Genome Sequencing

After annotating Pgenerosa_v074 and comparing feature counts, there was a drastic difference between the two genome versions. Additionally, both of those genomes ended up…

<<<<<<< HEAD

Essentially, the steps below (which is what was done here) are needed to prepare files for use with Stringtie:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genome Annotation - Pgenerosa_v074 Hisat2 Transcript Isoform Index

2019

Geoduck Genome Sequencing

Essentially, the steps below (which is what was done here) are needed to prepare files for use with Stringtie:

<<<<<<< HEAD

This is the first step in getting transcript isoform annotations. The annotations and alignments that will be generated with Stringtie will be used to help us get a better…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genome Annotation - Pgenerosa_v070 Hisat2 Transcript Isoform Index

2019

Geoduck Genome Sequencing

This is the first step in getting transcript isoform annotations. The annotations and alignments that will be generated with Stringtie will be used to help us get a better…

<<<<<<< HEAD

After annotating Pgenerosa_v074 on 20190701, we noticed a large discrepancy in the number of transcripts that MAKER identified, compared to Pgenerosa_v070. As a reminder…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genome Annotation - Pgenerosa_v070 and v074 Top 18 Scaffolds Feature Count Comparisons

2019

Geoduck Genome Sequencing

Jul 22, 2019

After annotating Pgenerosa_v074 on 20190701, we noticed a large discrepancy in the number of transcripts that MAKER identified, compared to Pgenerosa_v070. As a reminder…

<<<<<<< HEAD

Jul 22, 2019

Earlier today, I generated the necessary Hista2 index, which incorporated splice sites and exons, for use with Stringtie in order to identify transcript isoforms in our 20190…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genome Annotation - O.lurida 20190709-v081 Transcript Isoform ID with Stringtie on Mox

2019

Olympia Oyster Genome Sequencing

Earlier today, I generated the necessary Hista2 index, which incorporated splice sites and exons, for use with Stringtie in order to identify transcript isoforms in our 20190…

<<<<<<< HEAD

Last week I re-annotated our Olurida_v081 genome using tissue-specific transcriptomes. The MAKER annotations don’t yield transcript isoforms, so this is the first part of…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genome Annotation - O.lurida 20190709-v081 Hisat2 Transcript Isoform Index

2019

Olympia Oyster Genome Sequencing

Last week I re-annotated our Olurida_v081 genome using tissue-specific transcriptomes. The MAKER annotations don’t yield transcript isoforms, so this is the first part of…

<<<<<<< HEAD

Ran BUSCO on Mox for our Pgenerosa_v74 genome assembly to assess “completeness”. This is the assembly that only has the longest 18 scaffolds (the scaffolds hand-curated by…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genome Assessment - BUSCO Metazoa on Pgenerosa_v074 on Mox

2019

Geoduck Genome Sequencing

Ran BUSCO on Mox for our Pgenerosa_v74 genome assembly to assess “completeness”. This is the assembly that only has the longest 18 scaffolds (the scaffolds hand-curated by…

<<<<<<< HEAD

Ran BUSCO on Mox for our Pgenerosa_v70 genome assembly to assess “completeness”.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genome Assessment - BUSCO Metazoa on Pgenerosa_v70 on Mox

2019

Geoduck Genome Sequencing

Ran BUSCO on Mox for our Pgenerosa_v70 genome assembly to assess “completeness”.

<<<<<<< HEAD

In our various attempts to get the Panopea generosa genome annotated in such a manner that we’re comfortable with (the previous annotation attempts we’re lacking any…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genome Annotation - Pgenerosa_v071 Using GenSAS

2019

Geoduck Genome Sequencing

In our various attempts to get the Panopea generosa genome annotated in such a manner that we’re comfortable with (the previous annotation attempts we’re lacking any…

<<<<<<< HEAD

In our various attempts to get the Panopea generosa genome annotated in such a manner that we’re comfortable with (the previous annotation attempts we’re lacking any…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genome Annotation - Pgenerosa_v074 Using GenSAS

2019

Geoduck Genome Sequencing

In our various attempts to get the Panopea generosa genome annotated in such a manner that we’re comfortable with (the previous annotation attempts we’re lacking any…

<<<<<<< HEAD

I previously annotated our Olurida_v081 genome with MAKER using our “canonical” transcriptome, Olurida_transcriptome_v3.fasta as the EST evidence utilized by MAKER. A discuss…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genome Annotation - Olurida_v081 with MAKER and Tissue-specific Transcriptomes on Mox

2019

Olympia Oyster Genome Sequencing

Jul 9, 2019

I previously annotated our Olurida_v081 genome with MAKER using our “canonical” transcriptome, Olurida_transcriptome_v3.fasta as the EST evidence utilized by MAKER. A discuss…

<<<<<<< HEAD

Jul 9, 2019

I previously created a subset of the Pgenerosa_v070 genome assembly that contains just the largest 18 scaffolds (these scaffolds were produced by Phase Genomics, utilizing…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genome Annotation - Pgenerosa_v074 MAKER on Mox

2019

Geoduck Genome Sequencing

Jul 1, 2019

I previously created a subset of the Pgenerosa_v070 genome assembly that contains just the largest 18 scaffolds (these scaffolds were produced by Phase Genomics, utilizing…

<<<<<<< HEAD

Jul 1, 2019

Used Transdecoder to identify open reading frames (ORFs) for use in annotating Pgenerosa_v074 genome assembly. Relies on BLASTp, Pfam, and HMM scanning to ID ORFs.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Annotation - Geoduck Juvenile Ambient OA EPI124 with Transdecoder on Mox

2019

Miscellaneous

<<<<<<< HEAD

=======

Used Transdecoder to identify open reading frames (ORFs) for use in annotating Pgenerosa_v074 genome assembly. Relies on BLASTp, Pfam, and HMM scanning to ID ORFs. >>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

<<<<<<< HEAD

Used Transdecoder to identify open reading frames (ORFs) for use in annotating Pgenerosa_v074 genome assembly. Relies on BLASTp, Pfam, and HMM scanning to ID ORFs.

Transcriptome Annotation - Geoduck Super Low OA EPI116 with Transdecoder on Mox

2019

Miscellaneous

Used Transdecoder to identify open reading frames (ORFs) for use in annotating Pgenerosa_v074 genome assembly. Relies on BLASTp, Pfam, and HMM scanning to ID ORFs.

Transcriptome Annotation - Geoduck Ctenidia with Transdecoder on Mox

2019

Miscellaneous

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Used Transdecoder to identify open reading frames (ORFs) for use in annotating Pgenerosa_v074 genome assembly. Relies on BLASTp, Pfam, and HMM scanning to ID ORFs.

<<<<<<< HEAD

Used Transdecoder to identify open reading frames (ORFs) for use in annotating Pgenerosa_v074 genome assembly. Relies on BLASTp, Pfam, and HMM scanning to ID ORFs.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Annotation - Geoduck Juvenile Ambient OA EPI123 with Transdecoder on Mox

2019

Miscellaneous

<<<<<<< HEAD

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Used Transdecoder to identify open reading frames (ORFs) for use in annotating Pgenerosa_v074 genome assembly. Relies on BLASTp, Pfam, and HMM scanning to ID ORFs.

<<<<<<< HEAD

Used Transdecoder to identify open reading frames (ORFs) for use in annotating Pgenerosa_v074 genome assembly. Relies on BLASTp, Pfam, and HMM scanning to ID ORFs.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Annotation - Geoduck Larvae Day5 EPI99 with Transdecoder on Mox

2019

Miscellaneous

Used Transdecoder to identify open reading frames (ORFs) for use in annotating Pgenerosa_v074 genome assembly. Relies on BLASTp, Pfam, and HMM scanning to ID ORFs.

Transcriptome Annotation - Geoduck Gonad with Transdecoder on Mox

2019

Miscellaneous

Used Transdecoder to identify open reading frames (ORFs) for use in annotating Pgenerosa_v074 genome assembly. Relies on BLASTp, Pfam, and HMM scanning to ID ORFs.

Transcriptome Annotation - Geoduck Juvenile Super Low OA EPI115 with Transdecoder on Mox

2019

Miscellaneous

Used Transdecoder to identify open reading frames (ORFs) for use in annotating Pgenerosa_v074 genome assembly. Relies on BLASTp, Pfam, and HMM scanning to ID ORFs.

Transcriptome Annotation - Geoduck Super Low OA EPI116 with Transdecoder on Mox

2019

Miscellaneous

Used Transdecoder to identify open reading frames (ORFs) for use in annotating Pgenerosa_v074 genome assembly. Relies on BLASTp, Pfam, and HMM scanning to ID ORFs.

Transcriptome Annotation - Geoduck Ctenidia with Transdecoder on Mox

2019

Miscellaneous

Yesterday (20190625) I generated a subset of the first 18 FastA sequences from the Pgenerosa_v070.fa file. This subset has been designated as Pgenerosa_v074 by Steven. It’s…

RepeatModeler - Pgenerosa_v074 for MAKER Annotation on Emu

2019

Miscellaneous

Yesterday (20190625) I generated a subset of the first 18 FastA sequences from the Pgenerosa_v070.fa file. This subset has been designated as Pgenerosa_v074 by Steven. It’s…

<<<<<<< HEAD

Yesterday (20190625) I generated a subset of the first 18 FastA sequences from the Pgenerosa_v070.fa file. This subset has been designated as Pgenerosa_v074 by Steven. It’s…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RepeatMasker - Pgenerosa_v074 for Transposable Element ID on Roadrunner

2019

Miscellaneous

Yesterday (20190625) I generated a subset of the first 18 FastA sequences from the Pgenerosa_v070.fa file. This subset has been designated as Pgenerosa_v074 by Steven. It’s…

<<<<<<< HEAD

We received the BSseq data from ZymoResearch today. Samples were submitted on 20190326. The samples constituted 24 Crassostrea virginica mantle samples which were prepared…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Received - C.virginica Mantle MBD-BSseq from ZymoResearch

2019

Miscellaneous

We received the BSseq data from ZymoResearch today. Samples were submitted on 20190326. The samples constituted 24 Crassostrea virginica mantle samples which were prepared…

<<<<<<< HEAD

Steven asked to subset the Pgenerosa_v070.fa (2.1GB) in this GitHub Issue #705. In that issue, it was determined that a significant portion of the sequencing data that was…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Wrangling - FastA Subsetting of Pgenerosa_v070.fa Using samtools faidx

2019

Miscellaneous

Steven asked to subset the Pgenerosa_v070.fa (2.1GB) in this GitHub Issue #705. In that issue, it was determined that a significant portion of the sequencing data that was…

<<<<<<< HEAD

Earlier today, I generated the necessary Hista2 index, which incorporated splice sites and exons, for use with Stringtie in order to identify transcript isoforms in our Oluri…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genome Annotation - O.lurida (v081) Transcript Isoform ID with Stringtie on Mox

2019

Olympia Oyster Genome Sequencing

Earlier today, I generated the necessary Hista2 index, which incorporated splice sites and exons, for use with Stringtie in order to identify transcript isoforms in our Oluri…

<<<<<<< HEAD

Per this thread in Slack, we realized that the “final” annotation of the Olurida_v081 genome only seemed to have singular mRNA annotations and no apparent isoforms. As such…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genome Annotation - O.lurida (v081) Hisat2 Transcript Isoforms Index

2019

Olympia Oyster Genome Sequencing

Per this thread in Slack, we realized that the “final” annotation of the Olurida_v081 genome only seemed to have singular mRNA annotations and no apparent isoforms. As such…

<<<<<<< HEAD

UPDATE 20220121: THIS IS AN INCOMPLETE POST AND IS ONLY POSTED FOR POSTERITY.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Metagenomics - Refining Anvio Binning

2019

Miscellaneous

Jun 19, 2019

UPDATE 20220121: THIS IS AN INCOMPLETE POST AND IS ONLY POSTED FOR POSTERITY.

<<<<<<< HEAD

Jun 19, 2019

After a meeting on this project around the middle of May, we decided to try various approaches to assessing the metagenome. One aspect was to add coverage sequencing…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Metagenomics - Taxonomic Diversity and Sequencing Coverage with MEGAHIT BLASTx and Krona Plots

2019

Miscellaneous

Jun 12, 2019

After a meeting on this project around the middle of May, we decided to try various approaches to assessing the metagenome. One aspect was to add coverage sequencing…

<<<<<<< HEAD

Jun 12, 2019

Since the MAKER genome annotation of our Pgenerosa_v070 genome assembly finally completed last week, I decided to separate out the various features into separate GFF files…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Wrangling - Create Pgenerosa_v070 GFFs

2019

Geoduck Genome Sequencing

May 23, 2019

Since the MAKER genome annotation of our Pgenerosa_v070 genome assembly finally completed last week, I decided to separate out the various features into separate GFF files…

<<<<<<< HEAD

May 23, 2019

After reviewing our options for sample pooling, we decided to do a comparison of Infected vs. Uninfected crabs.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Sample Submission - Tanner Crab Infected vs Uninfected RNAseq

2019

Tanner Crab RNAseq

Samples Submitted

May 21, 2019

After reviewing our options for sample pooling, we decided to do a comparison of Infected vs. Uninfected crabs.

<<<<<<< HEAD

May 21, 2019

After a meeting on this project yesterda, we decided to try a few things to continue with various approaches to assessing the metagenome. One of the approaches is to run…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Metagenomics - BLASTx of Individual Water Sample MEGAHIT Assemblies on Mox

2019

Miscellaneous

May 16, 2019

After a meeting on this project yesterda, we decided to try a few things to continue with various approaches to assessing the metagenome. One of the approaches is to run…

<<<<<<< HEAD

May 16, 2019

I isolated a bunch of tanner crab RNA on 20190430 and Steven asked me to try to figure out some options for RNAseq libray pools.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Library Decisions - C.bairdi RNAs for Library Pools

2019

Tanner Crab RNAseq

May 14, 2019

I isolated a bunch of tanner crab RNA on 20190430 and Steven asked me to try to figure out some options for RNAseq libray pools.

<<<<<<< HEAD

May 14, 2019

Earlier today, we received the additional G.gigas sequencing data from Genewiz. Wanted to run through FastQC again and get an updated report for each data set. Admittedly…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

FastQC-MultiQC - Additional C.gigas WGBS Sequencing Data from Genewiz Received 20190501

2019

Miscellaneous

Earlier today, we received the additional G.gigas sequencing data from Genewiz. Wanted to run through FastQC again and get an updated report for each data set. Admittedly…

<<<<<<< HEAD

The FastQC analysis of the intitial data we received from Genewiz (on 20190408)showed consistent failures in the “Per Tile Sequence Quality” for all of Roberto’s Crassostrea…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Received - Additional C.gigas Whole Genome Bisulfite Sequencing Data from Genewiz

2019

Miscellaneous

The FastQC analysis of the intitial data we received from Genewiz (on 20190408)showed consistent failures in the “Per Tile Sequence Quality” for all of Roberto’s Crassostrea…

<<<<<<< HEAD

After the success we had isolating RNA using the Quick-DNA/RNA Microprep Plus Kit (ZymoResearch), Steven had me isolate RNA from a list of ~117 samples. Of that list, I was…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation and Quantification - C.bairdi Hemolymph Pellet in RNAlater

2019

Miscellaneous

Apr 30, 2019

After the success we had isolating RNA using the Quick-DNA/RNA Microprep Plus Kit (ZymoResearch), Steven had me isolate RNA from a list of ~117 samples. Of that list, I was…

<<<<<<< HEAD

Apr 30, 2019

Submitted the 10x Genomics sequencing files to the NCBI short read archive (SRA) that was performed by Illumina, as part of their generous offer to use geoduck samples to…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

SRA Submission - P.generosa 10x Genomics Sequencing Data

2019

Geoduck Genome Sequencing

Apr 24, 2019

Submitted the 10x Genomics sequencing files to the NCBI short read archive (SRA) that was performed by Illumina, as part of their generous offer to use geoduck samples to…

<<<<<<< HEAD

Apr 24, 2019

A while ago, Steven tasked me with assessing some questions related to the sequencing coverage we get doing MBD-BSseq in this GitHub issue. At the heart of it all was really…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Analysis - C.virginica MBD Sequencing Coverage

2019

Miscellaneous

Apr 18, 2019

A while ago, Steven tasked me with assessing some questions related to the sequencing coverage we get doing MBD-BSseq in this GitHub issue. At the heart of it all was really…

<<<<<<< HEAD

Apr 18, 2019

Nearing the end of this quick metagenomics comparison of taxonomic differences between the two pH treatments (pH=7.1 and pH=8.2). Previously ran:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Metagenomics Annotation - P.generosa Water Samples Using BLASTn on Mox and KronaTools Visualization to Compare pH Treatments

2019

Miscellaneous

Nearing the end of this quick metagenomics comparison of taxonomic differences between the two pH treatments (pH=7.1 and pH=8.2). Previously ran:

<<<<<<< HEAD

Continuing with a relatively quick comparison of pH treatments (pH=7.1 vs. pH=8.2), I wanted to run gene prediction on the MEGAHIT assemblies I made yesterday. I ran MetaGene…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Metagenomics Gene Prediction - P.generosa Water Samples Using MetaGeneMark on Mox to Compare pH Treatments

2019

Miscellaneous

Continuing with a relatively quick comparison of pH treatments (pH=7.1 vs. pH=8.2), I wanted to run gene prediction on the MEGAHIT assemblies I made yesterday. I ran MetaGene…

<<<<<<< HEAD

We received whole genome bisulfite sequencing (WGBS) data from Genewiz last week on 20190408, so ran FastQC on the files on my computer (swoose). FastQC results will be…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

FastQC - WGBS Sequencing Data from Genewiz Received 20190408

2019

Miscellaneous

We received whole genome bisulfite sequencing (WGBS) data from Genewiz last week on 20190408, so ran FastQC on the files on my computer (swoose). FastQC results will be…

<<<<<<< HEAD

A report involving our work on the geoduck water metagenomics is due later this week and our in-depth analysis for this project using Anvi’o is likely to require at least…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Metagenome Assemblies - P.generosa Water Samples Trimmed HiSeqX Data Using Megahit on Mox to Compare pH Treatments

2019

Miscellaneous

A report involving our work on the geoduck water metagenomics is due later this week and our in-depth analysis for this project using Anvi’o is likely to require at least…

<<<<<<< HEAD

In the continuing struggle to isolate RNA from the Chionoecetes bairdi hemolymph preserved in RNAlater, Pam managed to find the Quick-DNA-RNA Microprep Plus Kit…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation and Quantification - Crab Hemolypmh Using Quick-DNA-RNA Microprep Plus Kit

2019

Tanner Crab RNAseq

Apr 11, 2019

In the continuing struggle to isolate RNA from the Chionoecetes bairdi hemolymph preserved in RNAlater, Pam managed to find the Quick-DNA-RNA Microprep Plus Kit…

<<<<<<< HEAD

Apr 11, 2019

I previously assembled and annotated P.generosa larval Day 5 transcriptome (20190318 - mislabeled as Juvenile Day 5 in my previous notebook entries) using just our HiSeq…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Assembly - Geoduck Tissue-specific Assembly Larvae Day5 EPI99 with HiSeq and NovaSeq Data on Mox

2019

Miscellaneous

I previously assembled and annotated P.generosa larval Day 5 transcriptome (20190318 - mislabeled as Juvenile Day 5 in my previous notebook entries) using just our HiSeq…

<<<<<<< HEAD

I previously assembled and annotated P.generosa gonad transcriptome (20190318) using just our HiSeq data from our Illumina collaboration. This was a an oversight, as I…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Assembly - Geoduck Tissue-specific Assembly Gonad HiSeq and NovaSeq Data on Mox

2019

Miscellaneous

I previously assembled and annotated P.generosa gonad transcriptome (20190318) using just our HiSeq data from our Illumina collaboration. This was a an oversight, as I…

<<<<<<< HEAD

Ran a de novo assembly on our HiSeq and NovaSeq data from Hollie’s juvenile EPI 124 sample “ambient OA”. This was done for Christian to use in some long, non-coding RNA…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Assembly - Geoduck Tissue-specific Assembly Juvenile Ambient OA EPI124 with HiSeq and NovaSeq Data on Mox

2019

Miscellaneous

Ran a de novo assembly on our HiSeq and NovaSeq data from Hollie’s juvenile EPI 124 sample “ambient OA”. This was done for Christian to use in some long, non-coding RNA…

<<<<<<< HEAD

Ran a de novo assembly on our HiSeq data from Hollie’s juvenile EPI 123 sample “ambient OA”. This was done for Christian to use in some long, non-coding RNA (lncRNA) analysis.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Assembly - Geoduck Tissue-specific Assembly Juvenile Ambient OA EPI123 with HiSeq Data on Mox

2019

Miscellaneous

Ran a de novo assembly on our HiSeq data from Hollie’s juvenile EPI 123 sample “ambient OA”. This was done for Christian to use in some long, non-coding RNA (lncRNA) analysis.

<<<<<<< HEAD

Ran a de novo assembly on our HiSeq and NovaSeq data from Hollie’s juvenile EPI 116 sample “super low OA”. This was done for Christian to use in some long, non-coding RNA…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Assembly - Geoduck Tissue-specific Assembly Juvenile Super Low OA EPI116 with HiSeq and NovaSeq Data on Mox

2019

Miscellaneous

Ran a de novo assembly on our HiSeq and NovaSeq data from Hollie’s juvenile EPI 116 sample “super low OA”. This was done for Christian to use in some long, non-coding RNA…

<<<<<<< HEAD

Ran a de novo assembly on our HiSeq data from Hollie’s juvenile EPI 115 sample “super low OA”. This was done for Christian to use in some long, non-coding RNA (lncRNA)…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Assembly - Geoduck Tissue-specific Assembly Juvenile Super Low OA EPI115 with HiSeq Data on Mox

2019

Miscellaneous

Ran a de novo assembly on our HiSeq data from Hollie’s juvenile EPI 115 sample “super low OA”. This was done for Christian to use in some long, non-coding RNA (lncRNA)…

<<<<<<< HEAD

I previously assembled and annotated P.generosa ctenidia transcriptome (20190318) using just our HiSeq data from our Illumina collaboration. This was a an oversight, as I…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Assembly - Geoduck Tissue-specific Assembly Ctenidia with HiSeq and NovaSeq Data on Mox

2019

Miscellaneous

I previously assembled and annotated P.generosa ctenidia transcriptome (20190318) using just our HiSeq data from our Illumina collaboration. This was a an oversight, as I…

<<<<<<< HEAD

Received the WGBS data from Genewiz that were sent to Genewiz for whole genome bisulfite sequencing on 20190207. These were from:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Management - Whole Genome Bisulfite Sequencing Data from Genewiz Received

2019

Miscellaneous

Received the WGBS data from Genewiz that were sent to Genewiz for whole genome bisulfite sequencing on 20190207. These were from:

<<<<<<< HEAD

Continuing work on the metagenomics project, Emma shared her “co-assembly”, so I figured it would be quick and easy to compare hers with mine and get a feel for how…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Metagenomics - P.generosa Water Sample Assembly Comparisons with Quast

2019

Miscellaneous

Continuing work on the metagenomics project, Emma shared her “co-assembly”, so I figured it would be quick and easy to compare hers with mine and get a feel for how…

<<<<<<< HEAD

As part of addressing this GitHub Issue on assessing taxonomic diversity in our metagenomics samples, I decided to compare the individual sample assemblies I made on…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Metagenomics - Geoduck Water Sample Assembly Comparisons with MetaQuast

2019

Miscellaneous

Apr 3, 2019

As part of addressing this GitHub Issue on assessing taxonomic diversity in our metagenomics samples, I decided to compare the individual sample assemblies I made on…

<<<<<<< HEAD

Apr 3, 2019

I decided to give Anvi’o a shot for this metagenomics analysis, as it seems ridiculously thorough and easy to use, with a nice-looking, interactive plotting interface.…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Metagenomics - Taxonomic Diversity Comparisons from Geoduck Water with Anvio on Mox

2019

Miscellaneous

Apr 1, 2019

I decided to give Anvi’o a shot for this metagenomics analysis, as it seems ridiculously thorough and easy to use, with a nice-looking, interactive plotting interface.…

<<<<<<< HEAD

Apr 1, 2019

I previously created a single metagenome assembly using all of the sequencing data from this project.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Metagenome Assemblies - P.generosa Water Samples Trimmed HiSeqX Data Using Megahit on Mox

2019

Miscellaneous

I previously created a single metagenome assembly using all of the sequencing data from this project.

<<<<<<< HEAD

Per this GitHub issue, I’m IDing transposable elements (TEs) in the Crassostrea gigas genome. Even though the C.gigas genome should be fully annotated, Steven wants a…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transposable Element Mapping - Crassostrea gigas Genome v9 Using RepeatMasker 4.07 on Roadrunner

2019

Miscellaneous

Per this GitHub issue, I’m IDing transposable elements (TEs) in the Crassostrea gigas genome. Even though the C.gigas genome should be fully annotated, Steven wants a…

<<<<<<< HEAD

Crassostrea virginica samples that were subjected to MBD enrichment (completed 20190319) were shipped, on dry ice, to ZymoResearch today for BSseq. They will perform…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Sample Submission - Lotterhos C.virginica Mantle MBD DNA to ZymoResearch for BSseq

2019

Miscellaneous

Crassostrea virginica samples that were subjected to MBD enrichment (completed 20190319) were shipped, on dry ice, to ZymoResearch today for BSseq. They will perform…

<<<<<<< HEAD

In preparation for some manuscripts, Steven asked that I get some geoduck RNAseq data upload to the NCBI sequencing read archive (SRA) in this GitHub Issue. Specifically, he…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Management - SRA Submission Panopea generosa Day 5 Larvae RNAseq

2019

Miscellaneous

In preparation for some manuscripts, Steven asked that I get some geoduck RNAseq data upload to the NCBI sequencing read archive (SRA) in this GitHub Issue. Specifically, he…

<<<<<<< HEAD

Continuing on getting the metagenomics sequencing project written up as a manuscript, Steven asked me to provide an overview of the taxonomic makeup of our metagenome…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Metagenomics - Taxonomic Diversity from Geoduck Water with BLASTn and Krona Plots

2019

Miscellaneous

Continuing on getting the metagenomics sequencing project written up as a manuscript, Steven asked me to provide an overview of the taxonomic makeup of our metagenome…

<<<<<<< HEAD

We’re working on getting the metagenomics sequencing project written up as a manuscript and Steven asked me to provide an overview of the taxonomic makeup of our metagenome…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Metagenomics - Taxonomic Diversity from Geoduck Water with BLASTp and Krona plots

2019

Miscellaneous

We’re working on getting the metagenomics sequencing project written up as a manuscript and Steven asked me to provide an overview of the taxonomic makeup of our metagenome…

<<<<<<< HEAD

Finished MBD enrichment on 20190312 using the MethylMiner kit. Since we were out of Qubit assay tubes, I could not quantify these samples when I initially completed the…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

MBD Enrichment - DNA Quantification of C.virginica MBD Samples from 20190312

2019

Miscellaneous

Mar 19, 2019

Finished MBD enrichment on 20190312 using the MethylMiner kit. Since we were out of Qubit assay tubes, I could not quantify these samples when I initially completed the…

<<<<<<< HEAD

Mar 19, 2019

I ran Trinotate (v3.1.1) on Mox to annotate the P.generosa larvae transcriptome I previously assembled with the HiSeq data from Illumina.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Annotation - Geoduck Juvenile Day 5 with Trinotate on Mox

2019

Miscellaneous

I ran Trinotate (v3.1.1) on Mox to annotate the P.generosa larvae transcriptome I previously assembled with the HiSeq data from Illumina.

<<<<<<< HEAD

I ran Trinotate (v3.1.1) on Mox to annotate the P.generosa heart transcriptome I previously assembled with the HiSeq data from Illumina.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Annotation - Geoduck Heart with Trinotate on Mox

2019

Miscellaneous

I ran Trinotate (v3.1.1) on Mox to annotate the P.generosa heart transcriptome I previously assembled with the HiSeq data from Illumina.

<<<<<<< HEAD

I ran Trinotate (v3.1.1) on Mox to annotate the P.generosa gonad transcriptome I previously assembled with the HiSeq data from Illumina.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Annotation - Geoduck Gonad with Trinotate on Mox

2019

Miscellaneous

<<<<<<< HEAD

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

I ran Trinotate (v3.1.1) on Mox to annotate the P.generosa gonad transcriptome I previously assembled with the HiSeq data from Illumina.

<<<<<<< HEAD

I ran Trinotate (v3.1.1) on Mox to annotate the P.generosa ctenidia transcriptome I previously assembled with the HiSeq data from Illumina.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Annotation - Geoduck Ctenidia with Trinotate on Mox

2019

Miscellaneous

I’ll be annotating the transcriptome assembly (from 20190215) using Trinotate and part of that process is having BLASTx output for the Trinity assembly, so have run BLASTx…

Transcriptome Annotation - Geoduck Heart with BLASTx on Mox

2019

Miscellaneous

I’ll be annotating the transcriptome assembly (from 20190215) using Trinotate and part of that process is having BLASTx output for the Trinity assembly, so have run BLASTx…

<<<<<<< HEAD

I’ll be annotating the transcriptome assembly (from 20190215) using Trinotate and part of that process is having BLASTx output for the Trinity assembly, so have run BLASTx…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Annotation - Geoduck Gonad with BLASTx on Mox

2019

Miscellaneous

I’ll be annotating the transcriptome assembly (from 20190215) using Trinotate and part of that process is having BLASTx output for the Trinity assembly, so have run BLASTx…

<<<<<<< HEAD

I’ll be annotating the transcriptome assembly (from 20190215) using Trinotate and part of that process is having BLASTx output for the Trinity assembly, so have run BLASTx…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Annotation - Geoduck Ctenidia with BLASTx on Mox

2019

Miscellaneous

I’ll be annotating the transcriptome assembly (from 20190215) using Trinotate and part of that process is having BLASTx output for the Trinity assembly, so have run BLASTx…

<<<<<<< HEAD

I’ll be annotating the transcriptome assembly (from 20190215) using Trinotate and part of that process is having BLASTx output for the Trinity assembly, so have run BLASTx…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Annotation - Geoduck Juvenile Day 5 with BLASTx on Mox

2019

Miscellaneous

I’ll be annotating the transcriptome assembly (from 20190215) using Trinotate and part of that process is having BLASTx output for the Trinity assembly, so have run BLASTx…

<<<<<<< HEAD

Continuing tissue-specific RNAseq. Using Transdecoder to identify open reading frames (ORFs). Relies on BLASTp, Pfam, and HMM scanning to ID ORFs.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Annotation - Geoduck Juvenile Day 5 with Transdecoder on Mox

2019

Miscellaneous

Continuing tissue-specific RNAseq. Using Transdecoder to identify open reading frames (ORFs). Relies on BLASTp, Pfam, and HMM scanning to ID ORFs.

<<<<<<< HEAD

Continuing tissue-specific RNAseq. Using Transdecoder to identify open reading frames (ORFs). Relies on BLASTp, Pfam, and HMM scanning to ID ORFs.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Annotation - Geoduck Gonad with Transdecoder on Mox

2019

Miscellaneous

Continuing tissue-specific RNAseq. Using Transdecoder to identify open reading frames (ORFs). Relies on BLASTp, Pfam, and HMM scanning to ID ORFs.

<<<<<<< HEAD

Continuing tissue-specific RNAseq. Using Transdecoder to identify open reading frames (ORFs). Relies on BLASTp, Pfam, and HMM scanning to ID ORFs.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Annotation - Geoduck Heart with Transdecoder on Mox

2019

Miscellaneous

Continuing tissue-specific RNAseq. Using Transdecoder to identify open reading frames (ORFs). Relies on BLASTp, Pfam, and HMM scanning to ID ORFs.

<<<<<<< HEAD

Continuing tissue-specific RNAseq. Using Transdecoder to identify open reading frames (ORFs). Relies on BLASTp, Pfam, and HMM scanning to ID ORFs.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Annotation - Geoduck Ctenidia with Transdecoder on Mox

2019

Miscellaneous

Continuing tissue-specific RNAseq. Using Transdecoder to identify open reading frames (ORFs). Relies on BLASTp, Pfam, and HMM scanning to ID ORFs.

<<<<<<< HEAD

Steven asked for the following analysis in this GitHub Issue using Yaamini’s C.virginica MBD samples:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Methylation Analysis - C.virginica Gonad MBD with Varying Read Subsets with Bismark on Mox

2019

Miscellaneous

Mar 13, 2019

Steven asked for the following analysis in this GitHub Issue using Yaamini’s C.virginica MBD samples:

<<<<<<< HEAD

Mar 13, 2019

In preparation for some a bisulfite analysis requested by Steven, I needed to make bisulfite genome with, and for, Bismark to use and wanted to use the same one Yaamini has…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Management - Create C.virginica Bisulfite Genome with Bismark on Mox

2019

Miscellaneous

In preparation for some a bisulfite analysis requested by Steven, I needed to make bisulfite genome with, and for, Bismark to use and wanted to use the same one Yaamini has…

<<<<<<< HEAD

After completing two rounds of MBD enrichment (first 12 samples on 20190307 and the second 12 samples on 20190311), I performed ethanol precipitation, per the MethylMiner…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

MBD Enrichment - Ethanol Precipitation of C.virginica MBD samples

2019

Miscellaneous

After completing two rounds of MBD enrichment (first 12 samples on 20190307 and the second 12 samples on 20190311), I performed ethanol precipitation, per the MethylMiner…

<<<<<<< HEAD

Last week I performed MBD enrichment on 12 of the 24 Lotterhos C.viriginica mantle DNA on samples I had sheared on 20190306. I proceeded with MBD enrichment using the…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

MBD Enrichment - C.virginica Sheared Mantle DNA from 20190306

2019

Miscellaneous

Mar 11, 2019

Last week I performed MBD enrichment on 12 of the 24 Lotterhos C.viriginica mantle DNA on samples I had sheared on 20190306. I proceeded with MBD enrichment using the…

<<<<<<< HEAD

Mar 11, 2019

Yesterday, I sheared the Lotterhos C.virginica gDNA in preparation for MBD enrichment. Today, I proceeded with MBD enrichment using the MethylMiner Kit (Invitrogen) on 12 of…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

MBD Enrichment - C.virginica Sheared Mantle DNA from 20190306

2019

Miscellaneous

Mar 7, 2019

Yesterday, I sheared the Lotterhos C.virginica gDNA in preparation for MBD enrichment. Today, I proceeded with MBD enrichment using the MethylMiner Kit (Invitrogen) on 12 of…

<<<<<<< HEAD

Mar 7, 2019

Crassostrea virginica mantle gDNA that had previously been isolated on 20181114 was evaluated for integrity via agaroase gel yesterday (20190305). Everything looked pretty…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Shearing & Bioanalyzer - Lotterhos C.virginica Mantle gDNA from 2018114

2019

Miscellaneous

Mar 6, 2019

Crassostrea virginica mantle gDNA that had previously been isolated on 20181114 was evaluated for integrity via agaroase gel yesterday (20190305). Everything looked pretty…

<<<<<<< HEAD

Mar 6, 2019

Checked DNA integrity of the Crassostrea virginica mantle gDNA I isolated on 20181114 in preparation for MBD enrichment. Detailed sample info and sample processing…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Agarose Gel - Lotterhos C.virginica Mantle DNA from 20181114

2019

Miscellaneous

Mar 5, 2019

Checked DNA integrity of the Crassostrea virginica mantle gDNA I isolated on 20181114 in preparation for MBD enrichment. Detailed sample info and sample processing…

<<<<<<< HEAD

Mar 5, 2019

A little while ago, we installed some additional hard drives in Gannet (Synology RS3618XS) with the intention of expanding the total storage space. However, the original set…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Management - Data Migration and Drive Expansion on Gannet

2019

Miscellaneous

Mar 4, 2019

A little while ago, we installed some additional hard drives in Gannet (Synology RS3618XS) with the intention of expanding the total storage space. However, the original set…

<<<<<<< HEAD

Mar 4, 2019

Ran BUSCO on our completed annotation of the P.generosa v071 genome (GFF) (subset of sequences >10kbp). See this notebook entry for genome annotation info. This provides a…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genome Assessment - BUSCO Metazoa on P.generosa v071 on Mox

2019

Miscellaneous

Mar 2, 2019

Ran BUSCO on our completed annotation of the P.generosa v071 genome (GFF) (subset of sequences >10kbp). See this notebook entry for genome annotation info. This provides a…

<<<<<<< HEAD

Mar 2, 2019

Here it goes, a massive undertaking of attempting to annotate the Pgenerosa_v070 genome (FastA; 2.1GB) using MAKER on Mox! I previously started this on 20190115, but killed…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genome Annotation - Pgenerosa_v070 MAKER on Mox

2019

Geoduck Genome Sequencing

Feb 28, 2019

Here it goes, a massive undertaking of attempting to annotate the Pgenerosa_v070 genome (FastA; 2.1GB) using MAKER on Mox! I previously started this on 20190115, but killed…

<<<<<<< HEAD

Feb 28, 2019

Steven tasked me with processing ~90 FastA files containing gene sequences from C.virginica in this GitHub Issue. He needed to determine the Observed/Expected (O/E) ratio of…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Wrangling - CpG OE Calculations on C.virginica Genes

2019

Miscellaneous

Feb 26, 2019

Steven tasked me with processing ~90 FastA files containing gene sequences from C.virginica in this GitHub Issue. He needed to determine the Observed/Expected (O/E) ratio of…

<<<<<<< HEAD

Feb 26, 2019

This is a quick and dirty (i.e. no adaptor/quality trimming) assessment of all of our Ostrea lurida bisulfite sequencing efforts to date in order to get a rough idea of the…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Methylation Analysis - O.lurida Bismark on Mox

2019

Miscellaneous

This is a quick and dirty (i.e. no adaptor/quality trimming) assessment of all of our Ostrea lurida bisulfite sequencing efforts to date in order to get a rough idea of the…

<<<<<<< HEAD

This is a quick and dirty (i.e. no adaptor/quality trimming) assessment of all of our Panopea generosa bisulfite sequencing efforts to date in order to get a rough idea of…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Methylation Analysis - P.generosa Bismark on Mox

2019

Miscellaneous

This is a quick and dirty (i.e. no adaptor/quality trimming) assessment of all of our Panopea generosa bisulfite sequencing efforts to date in order to get a rough idea of…

<<<<<<< HEAD

This is a quick and dirty (i.e. no adaptor/quality trimming) assessment of all of our Crassostrea irginica bisulfite sequencing efforts to date in order to get a rough idea…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Methylation Analysis - C.virginica

2019

Miscellaneous

This is a quick and dirty (i.e. no adaptor/quality trimming) assessment of all of our Crassostrea irginica bisulfite sequencing efforts to date in order to get a rough idea…

<<<<<<< HEAD

This is a quick and dirty (i.e. no adaptor/quality trimming) assessment of all of our Crassostrea gigas bisulfite sequencing efforts to date in order to get a rough idea of…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Methylation Analysis - C.gigas Bismark on Mox

2019

Miscellaneous

This is a quick and dirty (i.e. no adaptor/quality trimming) assessment of all of our Crassostrea gigas bisulfite sequencing efforts to date in order to get a rough idea of…

<<<<<<< HEAD

In preparation for some a quick and “dirty” bisulfite analysis, I needed to make bisulfite genomes with, and for, Bismark to use.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Management - Create C.virginica Bisulfite Genome with Bismark on Mox

2019

Crassostrea virginica

eastern oyster

mox

bismark

In preparation for some a quick and “dirty” bisulfite analysis, I needed to make bisulfite genomes with, and for, Bismark to use.

<<<<<<< HEAD

In preparation for some a quick and “dirty” bisulfite analysis, I needed to make bisulfite genomes with, and for, Bismark to use.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Management - Create C.gigas Bisulfite Genome with Bismark on Mox

2019

Miscellaneous

In preparation for some a quick and “dirty” bisulfite analysis, I needed to make bisulfite genomes with, and for, Bismark to use.

<<<<<<< HEAD

In preparation for some a quick and “dirty” bisulfite analysis, I needed to make bisulfite genomes with, and for, Bismark to use.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Management - Create Geoduck Bisulfite Genomes with Bismark on Mox

2019

Miscellaneous

In preparation for some a quick and “dirty” bisulfite analysis, I needed to make bisulfite genomes with, and for, Bismark to use.

<<<<<<< HEAD

Based on a discussion in this GitHub Issue, I’ve initiated some tissue-specific transcriptome assemblies with our current geoduck data.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Assembly - Geoduck Tissue-specific Assembly Juvenile Day 5

2019

Miscellaneous

Based on a discussion in this GitHub Issue, I’ve initiated some tissue-specific transcriptome assemblies with our current geoduck data.

<<<<<<< HEAD

Based on a discussion in this GitHub Issue, I’ve initiated some tissue-specific transcriptome assemblies with our current geoduck data.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Assembly - Geoduck Tissue-specific Assembly Heart

2019

Miscellaneous

Based on a discussion in this GitHub Issue, I’ve initiated some tissue-specific transcriptome assemblies with our current geoduck data.

<<<<<<< HEAD

Based on a discussion in this GitHub Issue, I’ve initiated some tissue-specific transcriptome assemblies with our current geoduck data.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Assembly - Geoduck Tissue-specific Assembly Gonad

2019

Miscellaneous

Based on a discussion in this GitHub Issue, I’ve initiated some tissue-specific transcriptome assemblies with our current geoduck data.

<<<<<<< HEAD

Based on a discussion in this GitHub Issue, I’ve initiated some tissue-specific transcriptome assemblies with our current geoduck data.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Assembly - Geoduck Tissue-specific Assembly Ctenidia

2019

Miscellaneous

Based on a discussion in this GitHub Issue, I’ve initiated some tissue-specific transcriptome assemblies with our current geoduck data.

<<<<<<< HEAD

With the P.generosa v070 annotation taking a very long time (due to the genome/transcriptome sizes, and, hitting some snags in the script I put together), Steven asked if I…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genome Annotation - Pgenerosa_v71 with MAKER on Mox

2019

Miscellaneous

Feb 13, 2019

With the P.generosa v070 annotation taking a very long time (due to the genome/transcriptome sizes, and, hitting some snags in the script I put together), Steven asked if I…

<<<<<<< HEAD

Feb 13, 2019

Steven asked to subset geoduck assembly in to >10kbp and >30kbp groups. Here are the commands, using faidx:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Sequence Subsetting - Pgenerosa_v70 Genome Assembly with faidx

2019

Miscellaneous

Feb 11, 2019

Steven asked to subset geoduck assembly in to >10kbp and >30kbp groups. Here are the commands, using faidx:

<<<<<<< HEAD

Feb 11, 2019

Sent Roberto’s 12 designated DNA samples for whole genome bisulfite sequencing (WGBS) to Genewiz. They will do all bisulfite conversion, library prep and sequencing…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Samples Submitted - Robertos C.gigas DNA for Whole Genome Bisulfite Sequencing (Genewiz)

2019

Samples Submitted

Feb 7, 2019

Sent Roberto’s 12 designated DNA samples for whole genome bisulfite sequencing (WGBS) to Genewiz. They will do all bisulfite conversion, library prep and sequencing…

<<<<<<< HEAD

Feb 7, 2019

Sample list is here (Google Sheet):

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Samples Received - C.virginica DNA and Tissues from Lotterhos Lab

2019

Samples Received

Jan 29, 2019

Sample list is here (Google Sheet):

<<<<<<< HEAD

Jan 29, 2019

Last week, I isolated DNA from all of Ronti’s ctenidia samples, however one sample (D18-C) didn’t isolate properly. So, I performed another isolation procedure with another…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Isolation and Quantification - Ronit’s C.gigas Ploidy Ctenidia

2019

Miscellaneous

Jan 23, 2019

Last week, I isolated DNA from all of Ronti’s ctenidia samples, however one sample (D18-C) didn’t isolate properly. So, I performed another isolation procedure with another…

<<<<<<< HEAD

Jan 23, 2019

Isolated DNA from the remaining ctenidia tissue samples from Ronit’s experiment (Google Sheet).

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Isolation - C.gigas Ploidy Experiment Ctenidia

2019

Miscellaneous

Jan 17, 2019

Isolated DNA from the remaining ctenidia tissue samples from Ronit’s experiment (Google Sheet).

<<<<<<< HEAD

Jan 17, 2019

Previously performed this analysis using the eukaryota_odb9 BUSCO database. Figured I’d give it another go using a more specific database, metazoa_odb9, for comparison.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Annotation - Olurida_v081 MAKER BUSCO Metazoa Augustus Training on Mox

2019

Olympia Oyster Genome Sequencing

Previously performed this analysis using the eukaryota_odb9 BUSCO database. Figured I’d give it another go using a more specific database, metazoa_odb9, for comparison.

<<<<<<< HEAD

Well, here we go! Initiating full-blown annotation of the Pgenerosa_v070 (FastA; 2.1GB), using MAKER (v.2.31.10) on Mox. This will perform the following:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Annotation - Geoduck Genome with MAKER Submitted to Mox

2019

Geoduck Genome Sequencing

Well, here we go! Initiating full-blown annotation of the Pgenerosa_v070 (FastA; 2.1GB), using MAKER (v.2.31.10) on Mox. This will perform the following:

<<<<<<< HEAD

I’ve previously run MAKER, followed by two round of SNAP gene predictions and now I’m going to throw a BUSCO/Augustus gene training & prediction in the mix to see how it…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Annotation - Olurida_v081 MAKER BUSCO (eukaryota_odb9) Augustus Training Submitted to Mox

2019

Olympia Oyster Genome Sequencing

Jan 14, 2019

I’ve previously run MAKER, followed by two round of SNAP gene predictions and now I’m going to throw a BUSCO/Augustus gene training & prediction in the mix to see how it…

<<<<<<< HEAD

Jan 14, 2019

Believe it or not, full, proper annotation of the Olympia oyster genome is nearly complete! Here’s where it stands:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Annotation - Olurida_v081 MAKER Functional Annotations on Mox

2019

Olympia Oyster Genome Sequencing

Jan 9, 2019

Believe it or not, full, proper annotation of the Olympia oyster genome is nearly complete! Here’s where it stands:

<<<<<<< HEAD

Jan 9, 2019

After getting through the initial MAKER annotation and SNAP gene predictions, and then renaming the sequences, I needed to run BLASTp on the FastA file produced by MAKER id…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Annotation - Olurida_v081 MAKER Proteins BLASTp on Mox

2019

Olympia Oyster Genome Sequencing

After getting through the initial MAKER annotation and SNAP gene predictions, and then renaming the sequences, I needed to run BLASTp on the FastA file produced by MAKER id…

<<<<<<< HEAD

Continuation of genome annotation of the Olympia oyster genome. Determined initial gene models using MAKER with two rounds of SNAP, relabeled with more user-friendly names…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Annotation - Olurida_v081 MAKER Proteins InterProScan5 on Mox

2019

Olympia Oyster Genome Sequencing

Continuation of genome annotation of the Olympia oyster genome. Determined initial gene models using MAKER with two rounds of SNAP, relabeled with more user-friendly names…

<<<<<<< HEAD

After getting through the initial MAKER annotation and SNAP gene predictions, I needed (wanted?) to simplify annotation names that will be easier to read and are in a more…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Annotation - Olurida_v081 MAKER ID Mapping

2019

Olympia Oyster Genome Sequencing

After getting through the initial MAKER annotation and SNAP gene predictions, I needed (wanted?) to simplify annotation names that will be easier to read and are in a more…

<<<<<<< HEAD

After assembline the metagenomic data yesterday, I needed to predict some genes. I did this using MetaGeneMark (v.3.38) and ran it on Mox.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Gene Prediction - HiSeqX Metagenomics from Geoduck Water Using MetaGeneMark on Mox

2019

Miscellaneous

Jan 3, 2019

After assembline the metagenomic data yesterday, I needed to predict some genes. I did this using MetaGeneMark (v.3.38) and ran it on Mox.

<<<<<<< HEAD

Jan 3, 2019

Attempting an assembly of our geoduck metagenomics HiSeqX data using Megahit (v.1.1.4) on a Mox node.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Metagenome Assembly - P.generosa Water Sample Trimmed HiSeqX Data Using Megahit on Mox

Panopea generosa

geoduck

megahit

mox

metagenome

assembly

2019

Miscellaneous

Attempting an assembly of our geoduck metagenomics HiSeqX data using Megahit (v.1.1.4) on a Mox node.

<<<<<<< HEAD

Steven asked that I split up a Crassostrea virginica VCF file:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

VCF Splitting - C.virginica VCF Using BCFtools

2019

Miscellaneous

Steven asked that I split up a Crassostrea virginica VCF file:

<<<<<<< HEAD

Yesterday, Ronit initiated DNA isolation from ctenidia samples from his experiment (Google Sheet) from the following four samples:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Isolation - C.gigas Ploidy Experiment Ctenidia

2018

Miscellaneous

Dec 20, 2018

Yesterday, Ronit initiated DNA isolation from ctenidia samples from his experiment (Google Sheet) from the following four samples:

<<<<<<< HEAD

Dec 20, 2018

Needed to generate a generate a species-specific repeat library for use with MAKER genome annotation using RepeatModeler and the Pgenerosa_v070.fa (see our Genomic Resources…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Repeat Library Construction - P.generosa RepeatModeler v1.0.11

emu

repeatmodeler

jupyter notebook

Panopea generosa

geoduck

Pgenerosa_v070.fa

2018

Geoduck Genome Sequencing

Dec 19, 2018

Needed to generate a generate a species-specific repeat library for use with MAKER genome annotation using RepeatModeler and the Pgenerosa_v070.fa (see our Genomic Resources…

<<<<<<< HEAD

Dec 19, 2018

Using the C.gigas cytochrome c oxidase (COX1) primers (SR IDs: 1713, 1714)I designed the other day, I ran a qPCR on a subset of Ronit’s diploid/triploid control/heat shocked…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Relative mitochondrial abundance in C.gigas diploids and triploids subjected to acute heat stress via COX1

qPCR

Crassostrea gigas

Pacific oyster

CFX Connect

SsoFast EVAGreen

COX1

2018

Miscellaneous

Dec 17, 2018

Using the C.gigas cytochrome c oxidase (COX1) primers (SR IDs: 1713, 1714)I designed the other day, I ran a qPCR on a subset of Ronit’s diploid/triploid control/heat shocked…

<<<<<<< HEAD

Dec 17, 2018

Apparently we’ve had some interest in the Pacific herring transcriptomes (liver and testes) we produced many years ago. As such, Steven asked that I do a quick BLASTx to…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

BLASTx - Clupea pallasii (Pacific herring) liver and testes transcriptomes on Mox

2018

Miscellaneous

Dec 12, 2018

Apparently we’ve had some interest in the Pacific herring transcriptomes (liver and testes) we produced many years ago. As such, Steven asked that I do a quick BLASTx to…

<<<<<<< HEAD

Dec 12, 2018

Steven tasked me with assembling our geoduck metagenomics HiSeqX data. The first part of the process is examining the quality of the sequencing reads, performing quality…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

FastQC and Trimming - Metagenomics (Geoduck) HiSeqX Reads from 20180809

2018

Miscellaneous

Steven tasked me with assembling our geoduck metagenomics HiSeqX data. The first part of the process is examining the quality of the sequencing reads, performing quality…

<<<<<<< HEAD

We’re attempting a quick & dirty comparison of relative mitochondria counts between diploid and triploid C.gigas, so needed a single-copy mitochondrial gene target for qPCR.…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Primer Design - Gigas COX1 using Primer3

2018

Miscellaneous

We’re attempting a quick & dirty comparison of relative mitochondria counts between diploid and triploid C.gigas, so needed a single-copy mitochondrial gene target for qPCR.…

<<<<<<< HEAD

Earlier today I made some cDNA from geoduck gonad RNA for use in this qPCR to test out the vitellogenin primers I designed on 20181129

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Geoduck gonad cDNA with vitellogenin primers

qPCR

CFX

2x SsoFast EVAgreen

geoduck

vtg

vitellogenin

Panopea generosa

gonad

2018

Earlier today I made some cDNA from geoduck gonad RNA for use in this qPCR to test out the vitellogenin primers I designed on 20181129

<<<<<<< HEAD

To be able to actually test the vitellegenin primers I made, I needed some geoduck cDNA.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Reverse Transcription - Geoduck gonad RNA pool

2018

Miscellaneous

To be able to actually test the vitellegenin primers I made, I needed some geoduck cDNA.

<<<<<<< HEAD

In preparation for designing primers for developing a geoduck vitellogenin qPCR assay, I annotated a de novo geoduck transcriptome assembly last week. Next up, identify…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Primer Design - Geoduck Vitellogenin using Primer3

2018

Miscellaneous

Nov 29, 2018

In preparation for designing primers for developing a geoduck vitellogenin qPCR assay, I annotated a de novo geoduck transcriptome assembly last week. Next up, identify…

<<<<<<< HEAD

Nov 29, 2018

Remarkably, I managed to burn through our Xsede computing resources and don’t have terribly much to show for it. Ooof! This is a major bummer, as it “only” takes ~8hrs for a…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Annotation - Olurida_v081 MAKER on Mox

Ostrea lurida

Olympia oyster

mox

MAKER

genome annotation

Olurida_v081

2018

Olympia Oyster Genome Sequencing

Nov 27, 2018

Remarkably, I managed to burn through our Xsede computing resources and don’t have terribly much to show for it. Ooof! This is a major bummer, as it “only” takes ~8hrs for a…

<<<<<<< HEAD

Nov 27, 2018

I was tasked with generating some qPCR primers to analyze vitellogenin expression in geoduck. In order to do so, I needed to annotate a geoduck transcriptome in order to…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Annotation - Geoduck Transcritpome with TransDecoder

TransDecoder

geoduck

Panopea generosa

annotation

transcriptome

mox

2018

Nov 21, 2018

I was tasked with generating some qPCR primers to analyze vitellogenin expression in geoduck. In order to do so, I needed to annotate a geoduck transcriptome in order to…

<<<<<<< HEAD

Nov 21, 2018

After confirming Ronit’s DNased RNA was free of gDNA, I quantified the DNased RNA from 20181115 using the Roberts Lab Qubit 3.0 and the Qubit hsRNA Assay.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Quantification - Ronit’s C.gigas DNased RNA from 20181115

RNA quantification

Qubit 3.0

Qubit hsRNA

Crassostrea gigas

pacific oyster

diploid

triploid

dessication

DNased RNA

2018

After confirming Ronit’s DNased RNA was free of gDNA, I quantified the DNased RNA from 20181115 using the Roberts Lab Qubit 3.0 and the Qubit hsRNA Assay.

<<<<<<< HEAD

Quantified Ronit’s DNased RNA earlier today and proceeded with reverse transcription using 100ng of DNased RNA with oligo dT primers (Promega) and M-MLV reverse…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Reverse Transcription - Ronit’s C.gigas DNased RNA from 20181115

reverse transcription

cDNA

MMLV

pacific oyster

Crassostrea gigas

diploid

triploid

dessication

2018

Quantified Ronit’s DNased RNA earlier today and proceeded with reverse transcription using 100ng of DNased RNA with oligo dT primers (Promega) and M-MLV reverse…

<<<<<<< HEAD

Ronit finished his RNA isolations for his ctenidia samples on 20181025 & 20181101, as well as quntification (he has no notebook entry for this, at this time). However, his…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNase - Ronit’s C.gigas Ctenidia RNA

2018

Miscellaneous

Ronit finished his RNA isolations for his ctenidia samples on 20181025 & 20181101, as well as quntification (he has no notebook entry for this, at this time). However, his…

<<<<<<< HEAD

After DNasing Ronit’s RNA earlier today, I needed to verify the RNA was free of any contaminating gDNA.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Ronit’s DNased C.gigas RNA with Elongation Factor Primers

2018

Miscellaneous

After DNasing Ronit’s RNA earlier today, I needed to verify the RNA was free of any contaminating gDNA.

<<<<<<< HEAD

Per this issue on GitHub, I installed the pre-formatted NCBI non-redudant (nr) nucleotide (nt) database on Mox.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Computing - Install NCBI nr nt BLAST Database on Mox

2018

Miscellaneous

<<<<<<< HEAD

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Nov 14, 2018

Per this issue on GitHub, I installed the pre-formatted NCBI non-redudant (nr) nucleotide (nt) database on Mox.

<<<<<<< HEAD

Nov 14, 2018

Isolated DNA from the Lotterhos Crassostrea virginica mantle samples received on 20181017 using the E.Z.N.A. Mollusc Kit, with the following modifications/notes:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Isolation and Quantification - Lotterhos C.virginica Mantle DNA

2018

Miscellaneous

Nov 14, 2018

Here we are - my new notebook!

My New Notebook

computing

wordpress

jekyll

onsnetwork

2018

Nov 8, 2018

Here we are - my new notebook!

<<<<<<< HEAD

Nov 8, 2018

In further attempts to improve our Ostrea lurida genome annotation, I decided to generate a species-specific repeat library for use with MAKER genome annotation using RepeatM…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Repeat Library Construction - O.lurida RepeatModeler v1.0.11

emu

repeatmodeler

jupyter notebook

Ostrea lurida

olympia oyster

2018

Olympia Oyster Genome Sequencing

Oct 22, 2018

In further attempts to improve our Ostrea lurida genome annotation, I decided to generate a species-specific repeat library for use with MAKER genome annotation using RepeatM…

<<<<<<< HEAD

Oct 22, 2018

IMPORTANT: The cDNA used for the qPCRs described below was a 1:5 dilution of Ronit’s cDNA made 20181017 with the following primers! Diluted cDNA was stored in his -20^oC box…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCRs - Ronit’s C.gigas ploidy/dessication/heat stress cDNA (1:5 dilution)

2018

Miscellaneous

Oct 18, 2018

IMPORTANT: The cDNA used for the qPCRs described below was a 1:5 dilution of Ronit’s cDNA made 20181017 with the following primers! Diluted cDNA was stored in his -20^oC box…

<<<<<<< HEAD

Oct 18, 2018

Sample sheet (Google Sheet):

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Samples Received - Crassostrea virginica (Eastern oyster) tissue from Lotterhos Lab (Northeastern University)

2018

Samples Received

Sample sheet (Google Sheet):

<<<<<<< HEAD

Proceeded with reverse transcription of [Ronit’s DNased ctenidia RNA (from 20181016)(2018-10-16-dnase-treatment-ronits-c-gigas-ploiyddessication-ctenidia-rna.html).

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Reverse Transcription - Ronit’s C.gigas DNased ctenidia RNA

2018

Miscellaneous

Proceeded with reverse transcription of [Ronit’s DNased ctenidia RNA (from 20181016)(2018-10-16-dnase-treatment-ronits-c-gigas-ploiyddessication-ctenidia-rna.html).

<<<<<<< HEAD

After I figured out the appropriate DNA and primers to use to detect gDNA in Crassostrea gigas samples, I checked Ronit’s [DNased ctenidia RNA (from…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Ronit’s DNAsed C.gigas Ploidy/Dessication RNA with elongation factor primers

2018

Miscellaneous

After I figured out the appropriate DNA and primers to use to detect gDNA in Crassostrea gigas samples, I checked Ronit’s [DNased ctenidia RNA (from…

<<<<<<< HEAD

The qPCR I ran earlier today to check for residual gDNA in Ronit’s DNased RNA turned out terribly, due to a combination of bad primers and, possibly, bad gDNA.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR – C.gigas primer and gDNA tests with 18s and EF1 primers

2018

BB15

BB16

cfx connect

Cg_18s_1644_F

Cg_18s_1750_R

Crassostrea gigas

EF1_qPCR_3'

EF1_qPCR_5'

Pacific oyster

qPCR

SRID 1168

SRID 1169

SRID 309

SRID 310

SsoFast EvaGreen Supermix

`Oct 16, 2018`{=html}

After DNasing Ronit’s RNA earlier today, I needed to check for any residual gDNA.

<<<<<<< HEAD

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Ronit’s DNAsed C.gigas Ploidy/Dessication RNA with 18s primers

2018

Miscellaneous

After DNasing Ronit’s RNA earlier today, I needed to check for any residual gDNA.

<<<<<<< HEAD

After quantifying Ronit’s RNA earlier today, I DNased them using the Turbo DNA-free Kit (Ambion), according to the manufacturer’s standard protocol.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNase Treatment - Ronit’s C.gigas Ploiyd/Dessication Ctenidia RNA

2018

Miscellaneous

After quantifying Ronit’s RNA earlier today, I DNased them using the Turbo DNA-free Kit (Ambion), according to the manufacturer’s standard protocol.

<<<<<<< HEAD

Last Friday, Ronit quantified 1:10 dilutions of the RNA I isolated on 20181003 and the RNA he finished isolating on 20181011, but two of the samples (D11-C, T10-C) were…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Quantification - Ronit’s C.gigas Ploidy/Dessication RNA

2018

Miscellaneous

Last Friday, Ronit quantified 1:10 dilutions of the RNA I isolated on 20181003 and the RNA he finished isolating on 20181011, but two of the samples (D11-C, T10-C) were…

<<<<<<< HEAD

We received Grace’s 100bp PE NovaSeq (Illumian) RNAseq data from the Northwest Genomics Center today.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Received - Chionoecetes bairdi RNAseq & FastQC Analysis

2018

Miscellaneous

We received Grace’s 100bp PE NovaSeq (Illumian) RNAseq data from the Northwest Genomics Center today.

<<<<<<< HEAD

Steven asked for some help trying to split a VCF in to individual VCF files.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

VCF Splitting with bcftools

2018

Miscellaneous

Steven asked for some help trying to split a VCF in to individual VCF files.

<<<<<<< HEAD

I previously isolated RNA from crab hemolymp from a lyophilized sample using TriReagent and Grace recently tried isolating RNA from crab hemolyph pellet (non-lyophilized)…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation - Tanner Crab Hemolymph Pellet in RNAlater using TriReagent

2018

Chionoecetes bairdi

Qubit 3.0

Qubit RNA HS

RNA

RNA isolation

RNA quantification

tanner crab

TriReagent

Oct 9, 2018

I previously isolated RNA from crab hemolymp from a lyophilized sample using TriReagent and Grace recently tried isolating RNA from crab hemolyph pellet (non-lyophilized)…

<<<<<<< HEAD

Oct 9, 2018

Isolated RNA from a subset of Ronit’s Crassostrea gigas ctenidia samples (see Ronit’s notebook for experiment deets):

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation - Ronit’s C.gigas diploid/triploid dessication/heat shock ctenidia tissues

2018

Miscellaneous

Isolated RNA from a subset of Ronit’s Crassostrea gigas ctenidia samples (see Ronit’s notebook for experiment deets):

<<<<<<< HEAD

Submitted our whole genome bisulfite sequencing data to NCBI Sequence Read Archive (SRA).

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

SRA Submission - Olymia oyster Whole Genome BS-seq Data

2018

Olympia oyster reciprocal transplant

Submitted our whole genome bisulfite sequencing data to NCBI Sequence Read Archive (SRA).

<<<<<<< HEAD

Steven recently saw an announcement that Microsoft R Open now handles multi-threaded processing (default R does not), so we were interested in trying it out. I installed…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Installation - Microsoft Machine Learning Server (Microsoft R Open) on Emu/Roadrunner R Studio Server

2018

Miscellaneous

Steven recently saw an announcement that Microsoft R Open now handles multi-threaded processing (default R does not), so we were interested in trying it out. I installed…

<<<<<<< HEAD

An issue with Emu cropped up a few weeks ago that was seemingly caused by upgrading from Ubuntu 16.04 to 18.04.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Ubuntu – Fix “No Video Signal” Issue on Emu

2018

Computer Servicing

An issue with Emu cropped up a few weeks ago that was seemingly caused by upgrading from Ubuntu 16.04 to 18.04.

<<<<<<< HEAD

Yesterday, I produced a bedgraph file of our Olympia oyster RNAseq data coverage using our Olurida_v081 genome.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Alignment & Bedgraph – Olympia oyster transcriptome with Olurida_v080 genome assembly

2018

Miscellaneous

Yesterday, I produced a bedgraph file of our Olympia oyster RNAseq data coverage using our Olurida_v081 genome.

<<<<<<< HEAD

I took the sorted BAM file from yesterday’s corrected RNAseq genome alignment and converted it to a bedgraph using BEDTools genomeCoverageBed tool.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Bedgraph – Olympia oyster transcriptome with Olurida_v081 genome assembly

2018

Miscellaneous

I took the sorted BAM file from yesterday’s corrected RNAseq genome alignment and converted it to a bedgraph using BEDTools genomeCoverageBed tool.

<<<<<<< HEAD

Yesterday’s attempt at producing a bedgraph was a failure and a prodcuct of a major brain fart. The worst part is that I was questioning what I was doing the entire time…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Alignment – Olympia oyster RNAseq reads aligned to genome with HISAT2

2018

Miscellaneous

Sep 25, 2018

Yesterday’s attempt at producing a bedgraph was a failure and a prodcuct of a major brain fart. The worst part is that I was questioning what I was doing the entire time…

<<<<<<< HEAD

Sep 25, 2018

Progress on generating bedgraphs from our Olympia oyster transcriptome continues.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Bedgraph - Olympia oyster transcriptome (FAIL)

2018

Miscellaneous

Sep 24, 2018

Progress on generating bedgraphs from our Olympia oyster transcriptome continues.

<<<<<<< HEAD

Sep 24, 2018

Progress on generating bedgraphs from our Olympia oyster transcriptome continues.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Alignment - Olympia oyster Trinity transcriptome aligned to genome with Bowtie2

2018

Miscellaneous

Progress on generating bedgraphs from our Olympia oyster transcriptome continues.

<<<<<<< HEAD

Used all of our current oly RNAseq data to assemble a transcriptome using Trinity.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Assembly - Olympia oyster RNAseq Data with Trinity

2018

Miscellaneous

Used all of our current oly RNAseq data to assemble a transcriptome using Trinity.

<<<<<<< HEAD

I previously ran two variations on the Bismark analysis for our Olympia oyster whole genome bisulfite sequencing data:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Methylation Analysis – Olympia Oyster Whole Genome BSseq Bismark Pipeline MethylKit Comparison

2018

Miscellaneous

Sep 18, 2018

I previously ran two variations on the Bismark analysis for our Olympia oyster whole genome bisulfite sequencing data:

<<<<<<< HEAD

Sep 18, 2018

Due to difficulties getting RNA from hemolymph samples stored in RNAlater, Grace is testing out lyophilizing samples before extraction. Who knows what impact this will have…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation - Lyophilized Tanner Crab Hemolymph in RNAlater

2018

Miscellaneous

Sep 17, 2018

Due to difficulties getting RNA from hemolymph samples stored in RNAlater, Grace is testing out lyophilizing samples before extraction. Who knows what impact this will have…

<<<<<<< HEAD

Sep 17, 2018

Ran Bismark using our high performance computing (HPC) node, Mox, with two different bowtie2 settings:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Methylation Analysis - Olympia Oyster Whole Genome BSseq Bismark Pipeline Comparison

2018

Miscellaneous

Sep 13, 2018

Ran Bismark using our high performance computing (HPC) node, Mox, with two different bowtie2 settings:

<<<<<<< HEAD

Sep 13, 2018

We previously received sea lice (Caligus tape) DNA from Cris Gallardo-Escarate at Universidad de Concepción.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Quantification - Sea Lice DNA from 20180523

2018

Miscellaneous

Sep 12, 2018

We previously received sea lice (Caligus tape) DNA from Cris Gallardo-Escarate at Universidad de Concepción.

<<<<<<< HEAD

Sep 12, 2018

Previously concatenated and analyzed our Crassostrea virginica oil spill MBDseq data with FastQC.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

TrimGalore/FastQC/MultiQC - C.virginica Oil Spill MBDseq Concatenated Sequences

2018

LSU C.virginica Oil Spill MBD BS Sequencing

Sep 11, 2018

Previously concatenated and analyzed our Crassostrea virginica oil spill MBDseq data with FastQC.

<<<<<<< HEAD

Sep 11, 2018

Per Steven’s request, I concatenated our Crassostrea virginica LSU oil spill MBDseq sequencing data and ran FastQC on the concatenated files.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Sequencing Data Analysis - C.virginica Oil Spill MBDseq Concatenation & FastQC

2018

LSU C.virginica Oil Spill MBD BS Sequencing

Sep 10, 2018

Per Steven’s request, I concatenated our Crassostrea virginica LSU oil spill MBDseq sequencing data and ran FastQC on the concatenated files.

<<<<<<< HEAD

Sep 10, 2018

The goal of this analysis was to compare the methylation profiles of Olympia oysters originating from a common population (Fidalgo Bay) that were raised in two different…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Methylation Analysis - Olympia oyster BSseq MethylKit Analysis

2018

bismark

BSseq

methylation

methylkit

Olympia oyster

Ostrea lurida

The goal of this analysis was to compare the methylation profiles of Olympia oysters originating from a common population (Fidalgo Bay) that were raised in two different…

<<<<<<< HEAD

Used all of our current geoduck RNAseq data to assemble a transcriptome using Trinity.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transcriptome Assembly - Geoduck RNAseq data

2018

Miscellaneous

Used all of our current geoduck RNAseq data to assemble a transcriptome using Trinity.

<<<<<<< HEAD

I previously ran this data through the Bismark pipeline and followed up with MethylKit analysis. MethylKit analysis revealed an extremely low number of differentially…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

FastQC/MultiQC/TrimGalore/MultiQC/FastQC/MultiQC - O.lurida WGBSseq for Methylation Analysis

2018

BSseq

FASTQC

mox

multiqc

olympia oyster

Ostrea lurida

TrimGalore!

trimming

Aug 30, 2018

I previously ran this data through the Bismark pipeline and followed up with MethylKit analysis. MethylKit analysis revealed an extremely low number of differentially…

<<<<<<< HEAD

Aug 30, 2018

Per this GitHub issue, I’m IDing transposable elements (TEs) in the Crassostrea virginica genome.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transposable Element Mapping – Crassostrea virginica Genome, Cvirginica_v300, using RepeatMasker 4.07

2018

Miscellaneous

Aug 28, 2018

Per this GitHub issue, I’m IDing transposable elements (TEs) in the Crassostrea virginica genome.

<<<<<<< HEAD

Aug 28, 2018

We received the final geoduck genome assembly data from Phase Genomics, in which they updated the assembly by performing some manual curation:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Assembly Stats – Geoduck Hi-C Final Assembly Comparison

2018

Geoduck Genome Sequencing

Aug 23, 2018

We received the final geoduck genome assembly data from Phase Genomics, in which they updated the assembly by performing some manual curation:

<<<<<<< HEAD

Aug 23, 2018

Bismark analysis of all of our current Olympia oyster (Ostrea lurida) DNA methylation high-throughput sequencing data.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Methylation Analysis - Bismark Pipeline on All Olympia oyster BSseq Datasets

2018

Miscellaneous

Aug 16, 2018

Bismark analysis of all of our current Olympia oyster (Ostrea lurida) DNA methylation high-throughput sequencing data.

<<<<<<< HEAD

Aug 16, 2018

FastQ files are being transferred to owl/nightingales/P_generosa.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Received - Geoduck Metagenome HiSeqX Data

2018

Miscellaneous

FastQ files are being transferred to owl/nightingales/P_generosa.

<<<<<<< HEAD

Isolated RNA from 40 Tanner crab hemolymph samples selected by Grace with the RNeasy Plus Micro Kit (Qiagen) according to the manufacturer’s protocol, with the following…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation & Quantificaiton - Tanner Crab Hemolymph

2018

Miscellaneous

Isolated RNA from 40 Tanner crab hemolymph samples selected by Grace with the RNeasy Plus Micro Kit (Qiagen) according to the manufacturer’s protocol, with the following…

<<<<<<< HEAD

Yesterday, I annotated our Olympia oyster genome using WQ-MAKER in just 7hrs!.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genome Annotation – Olympia oyster genome annotation results #02

2018

Olympia Oyster Genome Sequencing

Yesterday, I annotated our Olympia oyster genome using WQ-MAKER in just 7hrs!.

<<<<<<< HEAD

Yesterday, I annotated our Olympia oyster genome using WQ-MAKER in just 7hrs!.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genome Annotation - Olympia oyster genome annotation results #01

2018

Olympia Oyster Genome Sequencing

Yesterday, I annotated our Olympia oyster genome using WQ-MAKER in just 7hrs!.

<<<<<<< HEAD

Whoa! Genome annotation using Jetstream/WQ-MAKER that I started this morning is complete!! Only 7hrs!

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genome Annotation – Olympia oyster genome complete - brief note

2018

Olympia Oyster Genome Sequencing

Whoa! Genome annotation using Jetstream/WQ-MAKER that I started this morning is complete!! Only 7hrs!

<<<<<<< HEAD

Yesterday, our Xsede Startup Application (Google Doc) got approval for 100,000 Service Units (SUs) and 1TB of disk space on Xsede/Atmosphere/Jetstream (or, whatever it’s…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genome Annotation - Olympia oyster genome using WQ-MAKER Instance on Jetstream

2018

Olympia Oyster Genome Sequencing

annotation

Atmosphere

Cyverse

genome

JetStream

maker

olympia oyster

Ostrea lurida

wq-maker

Xsede

Yesterday, our Xsede Startup Application (Google Doc) got approval for 100,000 Service Units (SUs) and 1TB of disk space on Xsede/Atmosphere/Jetstream (or, whatever it’s…

<<<<<<< HEAD

Ran the four Tanner crab RNA samples that I isolated yesterday on the Seeb Lab Bioanalyzer 2100 (Agilent) using the RNA Pico 6000 Kit.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Bioanalyzer - Tanner Crab RNA Isolated with RNeasy Plus Mini Kit

2018

Miscellaneous

Aug 1, 2018

Ran the four Tanner crab RNA samples that I isolated yesterday on the Seeb Lab Bioanalyzer 2100 (Agilent) using the RNA Pico 6000 Kit.

<<<<<<< HEAD

Aug 1, 2018

In a continued attempt to figure out what we can do about the tanner crab RNA, Steven tasked me with using an RNeasy Kit to cleanup some existing RNA.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Cleanup - Tanner Crab RNA

2018

Miscellaneous

In a continued attempt to figure out what we can do about the tanner crab RNA, Steven tasked me with using an RNeasy Kit to cleanup some existing RNA.

<<<<<<< HEAD

Tanner crab RNA has proved a bit troublesome. As such, [Steven asked me to try isolating some RNA using the RNeasy Plus Mini Kit…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation - Tanner Crab Hemolymph Using RNeasy Plus Mini Kit

2018

Miscellaneous

Tanner crab RNA has proved a bit troublesome. As such, [Steven asked me to try isolating some RNA using the RNeasy Plus Mini Kit…

<<<<<<< HEAD

Per this GitHub Issue, Steven has cleared out files.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Mox – Over quota: Olympia oyster genome annotation progress (using Maker 2.31.10)

2018

Olympia Oyster Genome Sequencing

Jul 30, 2018

Per this GitHub Issue, Steven has cleared out files.

<<<<<<< HEAD

Jul 30, 2018

Grace had previously pooled a set of crab RNA in preparation for RNAseq. Yesterday, we/she concentrated the samples and then quantified them. Unfortunately, Qubit results…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Cleanup - Tanner Crab RNA Pools

2018

Tanner Crab RNAseq

Jul 19, 2018

Grace had previously pooled a set of crab RNA in preparation for RNAseq. Yesterday, we/she concentrated the samples and then quantified them. Unfortunately, Qubit results…

<<<<<<< HEAD

Jul 19, 2018

I decided to spend some time to figure out what was actually happening, as it’s clear that the annotation process is going to need some additional time to run and may span…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Mox - Olympia oyster genome annotation progress (using Maker 2.31.10)

2018

Olympia Oyster Genome Sequencing

I decided to spend some time to figure out what was actually happening, as it’s clear that the annotation process is going to need some additional time to run and may span…

<<<<<<< HEAD

The high performance computing (HPC) cluster (called Mox) at Univ. of Washington (UW) frustratingly requires a password when SSH-ing, even when SSH keys are in use. I have a…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Mox - Password-less SSH!

2018

Miscellaneous

The high performance computing (HPC) cluster (called Mox) at Univ. of Washington (UW) frustratingly requires a password when SSH-ing, even when SSH keys are in use. I have a…

<<<<<<< HEAD

Both Apple Xserves (Emu/Roadrunner) running Ubuntu (16.04LTS) experienced the same issue - the monitor would indicate “No Video Signal”, would go dark, and wasn’t responsive…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Ubuntu - Fix “No Video Signal” Issue on Emu/Roadrunner

2018

Computer Servicing

Jul 5, 2018

Both Apple Xserves (Emu/Roadrunner) running Ubuntu (16.04LTS) experienced the same issue - the monitor would indicate “No Video Signal”, would go dark, and wasn’t responsive…

<<<<<<< HEAD

Jul 5, 2018

I previously performed this analysis using a different version of our Ostrea lurida genome assembly. Steven asked that I repeat the analysis with a modified version of the…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transposable Element Mapping – Olympia Oyster Genome Assembly, Olurida_v081, using RepeatMasker 4.07

2018

Miscellaneous

Jul 3, 2018

I previously performed this analysis using a different version of our Ostrea lurida genome assembly. Steven asked that I repeat the analysis with a modified version of the…

<<<<<<< HEAD

Jul 3, 2018

Made Illumina libraries with goeduck metagenome water filter DNA I previously isolated on:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Library Construction - Geoduck Water Filter Metagenome with Nextera DNA Flex Kit (Illumina)

2018

bioanalyzer

geoduck

library prep

metagenomics

nextera

Panopea generosa

Qubit 1x dsDNA HS Assay Kit

Qubit 3.0

Jun 6, 2018

Made Illumina libraries with goeduck metagenome water filter DNA I previously isolated on:

<<<<<<< HEAD

Jun 6, 2018

Previously took the analysis just through the mapping, but didn’t realize Steven wanted me to fully process the data.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

BS-seq Mapping – Olympia oyster bisulfite sequencing: Bismark Continued

2018

Miscellaneous

May 31, 2018

Previously took the analysis just through the mapping, but didn’t realize Steven wanted me to fully process the data.

<<<<<<< HEAD

May 31, 2018

Genome used: NCBI GCA_002022765.4_C_virginica-3.0

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transposable Element Mapping – Crassostrea virginica NCBI Genome Assembly using RepeatMasker 4.07

2018

Miscellaneous

May 29, 2018

Genome used: NCBI GCA_002022765.4_C_virginica-3.0

<<<<<<< HEAD

May 29, 2018

Steven wanted transposable elements (TEs) in the Olympia oyster genome identified.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Read Mapping – Olympia oyster 2bRAD Data with Bowtie2 (on Mox)

2018

Miscellaneous

<<<<<<< HEAD

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Transposable Element Mapping - Olympia Oyster Genome Assembly using RepeatMasker 4.07

2018

Miscellaneous

Steven wanted transposable elements (TEs) in the Olympia oyster genome identified.

<<<<<<< HEAD

Received Caligus tape DNA - two samples:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Received - Sea lice DNA from Cris Gallardo-Escarate at Universidad de Concepción

2018

Samples Received

Received Caligus tape DNA - two samples:

<<<<<<< HEAD

After yesterday’s difficulties getting RMblast to compile, I deleted the folder and went through the build process again.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Software Installation – RepeatMasker v4.0.7 on Emu/Roadrunner Continued

2018

Miscellaneous

After yesterday’s difficulties getting RMblast to compile, I deleted the folder and went through the build process again.

<<<<<<< HEAD

Steven asked that I re-run some Olympia oyster transposable elements analysis using RepeatMasker and a newer version of our Olympia oyster genome assembly.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Software Installation - RepeatMasker v4.0.7 on Emu/Roadrunner

2018

emu

RepeatMasker

roadrunner

transposable elements

May 22, 2018

Steven asked that I re-run some Olympia oyster transposable elements analysis using RepeatMasker and a newer version of our Olympia oyster genome assembly.

<<<<<<< HEAD

May 22, 2018

Earlier this week, I ran TrimGalore!, but set the trimming, incorrectly - due to a copy/paste mistake, as --non-directional, so I re-ran with the correct settings.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

TrimGalore/FastQC/MultiQC – TrimGalore! RRBS Geoduck BS-seq FASTQ data (directional)

2018

Miscellaneous

Earlier this week, I ran TrimGalore!, but set the trimming, incorrectly - due to a copy/paste mistake, as --non-directional, so I re-ran with the correct settings.

<<<<<<< HEAD

Earlier today I finished trimming Hollie’s RRBS BS-seq FastQ data.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

FastQC - RRBS Geoduck BS-seq FASTQ data

2018

Miscellaneous

Earlier today I finished trimming Hollie’s RRBS BS-seq FastQ data.

<<<<<<< HEAD

Steven requested that I trim the Geoduck RRBS libraries that we have, in preparation to run them through Bismark.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

TrimGalore/FastQC/MultiQC – TrimGalore! RRBS Geoduck BS-seq FASTQ data

2018

Miscellaneous

Steven requested that I trim the Geoduck RRBS libraries that we have, in preparation to run them through Bismark.

<<<<<<< HEAD

As part of the Illumina collaborative geoduck genome sequencing project, their end goal has always been to sequence the genome in a single run.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Management - Illumina NovaSeq Geoduck Genome Sequencing

2018

Geoduck Genome Sequencing

As part of the Illumina collaborative geoduck genome sequencing project, their end goal has always been to sequence the genome in a single run.

<<<<<<< HEAD

Steven asked me to create a couple of subsets of our Phase Genomics Hi-C geoduck genome assembly (pga_02):

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Assembly - Geoduck Hi-C Assembly Subsetting

2018

Geoduck Genome Sequencing

May 12, 2018

Steven asked me to create a couple of subsets of our Phase Genomics Hi-C geoduck genome assembly (pga_02):

<<<<<<< HEAD

May 12, 2018

We have an upcoming meeting with Illumina to discuss how the geoduck genome project is coming along and to decide how we want to proceed.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Read Mapping - Mapping Illumina Data to Geoduck Genome Assemblies with Bowtie2

2018

Geoduck Genome Sequencing

May 9, 2018

We have an upcoming meeting with Illumina to discuss how the geoduck genome project is coming along and to decide how we want to proceed.

<<<<<<< HEAD

May 9, 2018

Steven asked me to evaluate our methylation sequencing data sets for Olympia oyster.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

BS-seq Mapping - Olympia oyster bisulfite sequencing: TrimGalore > FastQC > Bismark

2018

BS-seq Libraries for Sequencing at Genewiz

MBD Enrichment for Sequencing at ZymoResearch

May 8, 2018

Steven asked me to evaluate our methylation sequencing data sets for Olympia oyster.

<<<<<<< HEAD

May 8, 2018

Had a successful assembly with SparseAssembler k101, but figured I’d just tweak the kmer setting and throw it in the queue and see how it compares; minimal effort/time needed.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Assembly & Stats - SparseAssembler (k95) on Geoduck Sequence Data > Quast for Stats

2018

Geoduck Genome Sequencing

May 1, 2018

Had a successful assembly with SparseAssembler k101, but figured I’d just tweak the kmer setting and throw it in the queue and see how it compares; minimal effort/time needed.

<<<<<<< HEAD

May 1, 2018

Steven requested a comparison of geoduck genome assemblies.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Assembly Stats - Geoduck Genome Assembly Comparisons w/Quast - SparseAssembler, SuperNova, Hi-C

2018

Geoduck Genome Sequencing

Steven requested a comparison of geoduck genome assemblies.

<<<<<<< HEAD

Ran the following Quast command to compare the two geoduck assemblies provided to us by Phase Genomics:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Assembly Stats - Geoduck Hi-C Assembly Comparison

2018

Geoduck Genome Sequencing

Ran the following Quast command to compare the two geoduck assemblies provided to us by Phase Genomics:

<<<<<<< HEAD

After discussing the preliminary DNA isolation attemp with Steven & Emma, we decided to proceed with DNA isolations on the remaining 0.22μm filters.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Isolation & Quantification - Metagenomics Water Filters

2018

Miscellaneous

Apr 26, 2018

After discussing the preliminary DNA isolation attemp with Steven & Emma, we decided to proceed with DNA isolations on the remaining 0.22μm filters.

<<<<<<< HEAD

Apr 26, 2018

I ran a subset of Yaamini’s ocean chemistry samples on our T5 Excellence titrator (Mettler Toledo) at the beginning of April. The subset were samples taken from the…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Total Alkalinity Calculations - Yaamini’s Ocean Chemistry Samples

2018

Miscellaneous

Apr 24, 2018

I ran a subset of Yaamini’s ocean chemistry samples on our T5 Excellence titrator (Mettler Toledo) at the beginning of April. The subset were samples taken from the…

<<<<<<< HEAD

Apr 24, 2018

Continuing to try to find the best kmer setting to work with SparseAssemlber after the last attempt failed due to a kmer size that was too large (k 131; which happens to be…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Assembly – SparseAssembler (k 111) on Geoduck Sequence Data

2018

Geoduck Genome Sequencing

Apr 23, 2018

Continuing to try to find the best kmer setting to work with SparseAssemlber after the last attempt failed due to a kmer size that was too large (k 131; which happens to be…

<<<<<<< HEAD

Apr 23, 2018

After some runs with kmergenie, I’ve decided to try re-running SparseAssembler using a kmer setting of 131.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Assembly – SparseAssembler (k 131) on Geoduck Sequence Data

2018

Geoduck Genome Sequencing

Apr 22, 2018

After some runs with kmergenie, I’ve decided to try re-running SparseAssembler using a kmer setting of 131.

<<<<<<< HEAD

Apr 22, 2018

We received sequencing/assembly data from Phase Genomics.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Management - Geoduck Phase Genomics Hi-C Data

2018

Geoduck Genome Sequencing

Samples Received

We received sequencing/assembly data from Phase Genomics.

<<<<<<< HEAD

Continuing the quest for the ideal kmer size to use for our geoduck assembly.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Kmer Estimation – Kmergenie (k 301) on Geoduck Sequence Data

2018

Geoduck Genome Sequencing

Continuing the quest for the ideal kmer size to use for our geoduck assembly.

<<<<<<< HEAD

Earlier today, I ran kmergenie on our all of geoduck DNA sequencing data to see what it would spit out for an ideal kmer setting, which I would then use in another assembly…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Kmer Estimation – Kmergenie Tweaks on Geoduck Sequence Data

2018

Geoduck Genome Sequencing

geoduck

kmer

kmer genie

mox

Panopea generosa

Earlier today, I ran kmergenie on our all of geoduck DNA sequencing data to see what it would spit out for an ideal kmer setting, which I would then use in another assembly…

<<<<<<< HEAD

After the last SparseAssembler assembly completed, I wanted to do another run with a different kmer size (last time was arbitrarily set at 101). However, I didn’t really…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Kmer Estimation - Kmergenie on Geoduck Sequence Data (default settings)

2018

Geoduck Genome Sequencing

geoduck

kmer

kmer genie

mox

Panopea generosa

After the last SparseAssembler assembly completed, I wanted to do another run with a different kmer size (last time was arbitrarily set at 101). However, I didn’t really…

<<<<<<< HEAD

The geoduck genome assembly started 20180405 completed this weekend.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Assembly Stats - Quast Stats for Geoduck SparseAssembler Job from 20180405

2018

Geoduck Genome Sequencing

Apr 15, 2018

The geoduck genome assembly started 20180405 completed this weekend.

<<<<<<< HEAD

Apr 15, 2018

Submitted the Crassostrea virginica (Eastern oyster) MBD BS-seq data we received on 20150413 to NCBI Sequence Read Archive.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Management - SRA Submission LSU C.virginica Oil Spill MBD BS-seq Data

2018

LSU C.virginica Oil Spill MBD BS Sequencing

Apr 12, 2018

Submitted the Crassostrea virginica (Eastern oyster) MBD BS-seq data we received on 20150413 to NCBI Sequence Read Archive.

<<<<<<< HEAD

Apr 12, 2018

Steven found out that the Bismarck documentation (Bismarck is the bisulfite aligner we use in our BS-seq pipeline) suggests trimming 10bp from both the 5’ and 3’ ends. Since…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

TrimGalore/FastQC/MultiQC - Trim 10bp 5’/3’ ends C.virginica MBD BS-seq FASTQ data

2018

Crassostrea virginica

Eastern oyster

FASTQC

MBD-Seq

multiqc

TrimGalore!

ZymoResearch

Steven found out that the Bismarck documentation (Bismarck is the bisulfite aligner we use in our BS-seq pipeline) suggests trimming 10bp from both the 5’ and 3’ ends. Since…

<<<<<<< HEAD

Isolated DNA from the following two filters:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Isolation & Quantification - Metagenomics Water Filters

2018

Miscellaneous

Isolated DNA from the following two filters:

<<<<<<< HEAD

Earlier today, I ran TrimGalore/FastQC/MultiQC on the Crassostrea virginica MBD BS-seq data from ZymoResearch and hard trimmed the first 14bp from each read. Things looked…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

TrimGalore/FastQC/MultiQC - 2bp 3’ end Read 1s Trim C.virginica MBD BS-seq FASTQ data

2018

Crassostrea virginica

Eastern oyster

FASTQC

MBD-Seq

multiqc

TrimGalore!

ZymoResearch

Earlier today, I ran TrimGalore/FastQC/MultiQC on the Crassostrea virginica MBD BS-seq data from ZymoResearch and hard trimmed the first 14bp from each read. Things looked…

<<<<<<< HEAD

Yesterday, I ran TrimGalore/FastQC/MultiQC on the Crassostrea virginica MBD BS-seq data from ZymoResearch with the default settings (i.e. “auto-trim”). There was still some…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

TrimGalore/FastQC/MultiQC - 14bp Trim C.virginica MBD BS-seq FASTQ data

2018

Miscellaneous

Yesterday, I ran TrimGalore/FastQC/MultiQC on the Crassostrea virginica MBD BS-seq data from ZymoResearch with the default settings (i.e. “auto-trim”). There was still some…

<<<<<<< HEAD

Yesterday, I ran FastQC/MultiQC on the Crassostrea virginica MBD BS-seq data from ZymoResearch. Steven wanted to trim it and see how things turned out.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

TrimGalore/FastQC/MultiQC - Auto-trim C.virginica MBD BS-seq FASTQ data

2018

Miscellaneous

Yesterday, I ran FastQC/MultiQC on the Crassostrea virginica MBD BS-seq data from ZymoResearch. Steven wanted to trim it and see how things turned out.

<<<<<<< HEAD

Per Steven’s GitHub Issues request, I ran FastQC on the Eastern oyster MBD bisulfite sequencing data we recently got back from ZymoResearch.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

FastQC/MultiQC - C. virginica MBD BS-seq Data

2018

Miscellaneous

Per Steven’s GitHub Issues request, I ran FastQC on the Eastern oyster MBD bisulfite sequencing data we recently got back from ZymoResearch.

<<<<<<< HEAD

Assembly complete. See end of post for data locations.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genome Assembly - SparseAssembler Geoduck Genomic Data, kmer=101

2018

Geoduck Genome Sequencing

Assembly complete. See end of post for data locations.

<<<<<<< HEAD

In preparation to run SpareAssembler, I needed to gunzip the BGI gzipped FASTQ files from 20180327.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Gunzip - BGI HiSeq Geoduck Genome Sequencing Data

2018

Geoduck Genome Sequencing

In preparation to run SpareAssembler, I needed to gunzip the BGI gzipped FASTQ files from 20180327.

<<<<<<< HEAD

In preparation to run SpareAssembler, I needed to gunzip the trimmed gzipped FASTQ files from 20140401.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Gunzip - Trimmed Illumina Geoduck HiSeq Genome Sequencing Data

2018

Geoduck Genome Sequencing

Apr 4, 2018

In preparation to run SpareAssembler, I needed to gunzip the trimmed gzipped FASTQ files from 20140401.

<<<<<<< HEAD

Apr 4, 2018

This is another attempt to isolate DNA from two more of the geoduck hatchery metagenome samples Emma delivered on 20180313.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Isolation & Quantification – Geoduck larvae metagenome filter rinses

2018

Miscellaneous

This is another attempt to isolate DNA from two more of the geoduck hatchery metagenome samples Emma delivered on 20180313.

<<<<<<< HEAD

All data is deposited in the following GitHub repo:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Titrations - Yaamini’s Seawater Samples

2018

Miscellaneous

All data is deposited in the following GitHub repo:

<<<<<<< HEAD

All data is deposited in the following GitHub repo:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Titrations - Yaamini’s Seawater Samples

2018

Miscellaneous

Apr 2, 2018

All data is deposited in the following GitHub repo:

<<<<<<< HEAD

Apr 2, 2018

The previous attempt at this was interrupted by a random glitch with our Mox HPC node.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

TrimGalore!/FastQC/MultiQC - Illumina HiSeq Genome Sequencing Data Continued

2018

Geoduck Genome Sequencing

Apr 1, 2018

The previous attempt at this was interrupted by a random glitch with our Mox HPC node.

<<<<<<< HEAD

Apr 1, 2018

Received the sequencing data from ZymoResearch for the Crassostrea virginica gonad MBD DNA that was sent to them on 20180207 for bisulfite conversion, library construction…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Received - Crassostrea virginica MBD BS-seq from ZymoResearch

2018

Miscellaneous

Mar 29, 2018

Received the sequencing data from ZymoResearch for the Crassostrea virginica gonad MBD DNA that was sent to them on 20180207 for bisulfite conversion, library construction…

<<<<<<< HEAD

Mar 29, 2018

Since running SparseAssembler seems to be working and actually able to produce assemblies, I’ve decided I’ll try to beef up the geoduck genome assembly with the rest of our…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

FastQC/MultiQC – Illumina HiSeq Genome Sequencing Data

2018

Geoduck Genome Sequencing

Since running SparseAssembler seems to be working and actually able to produce assemblies, I’ve decided I’ll try to beef up the geoduck genome assembly with the rest of our…

<<<<<<< HEAD

Previous FastQC/MultiQC analysis of the geoduck Illumina HiSeq data (NMP.fastq.gz files) revealed a high level of overrepresented sequences, high levels of Per Base N…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

TrimGalore!/FastQC/MultiQC - Illumina HiSeq Genome Sequencing Data

2018

Geoduck Genome Sequencing

Previous FastQC/MultiQC analysis of the geoduck Illumina HiSeq data (NMP.fastq.gz files) revealed a high level of overrepresented sequences, high levels of Per Base N…

<<<<<<< HEAD

Since running SparseAssembler seems to be working and actually able to produce assemblies, I’ve decided I’ll try to beef up the geoduck genome assembly with the rest of our…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

FastQC/MultiQC - BGI Geoduck Genome Sequencing Data

2018

Geoduck Genome Sequencing

Since running SparseAssembler seems to be working and actually able to produce assemblies, I’ve decided I’ll try to beef up the geoduck genome assembly with the rest of our…

<<<<<<< HEAD

All data is deposited in the following GitHub repo:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Titrations - Hollie’s Seawater Samples

2018

Miscellaneous

All data is deposited in the following GitHub repo:

<<<<<<< HEAD

The prior run used a kmer size of 61, and the resulting assembly was rather poor (small N50).

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Assembly - Geoduck NovaSeq using SparseAssembler kmer = 101

2018

Geoduck Genome Sequencing

The prior run used a kmer size of 61, and the resulting assembly was rather poor (small N50).

<<<<<<< HEAD

The prior attempt using SparseAssembler failed due to a kmer size that was deemed too large.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Assembly - Geoduck NovaSeq using SparseAssembler (TL;DR - it worked!)

2018

Geoduck Genome Sequencing

Mar 22, 2018

The prior attempt using SparseAssembler failed due to a kmer size that was deemed too large.

<<<<<<< HEAD

Mar 22, 2018

All data is deposited in the following GitHub repo:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Titrations - Hollie’s Seawater Samples

2018

Miscellaneous

All data is deposited in the following GitHub repo:

<<<<<<< HEAD

Isolated DNA from two of the geoduck hatchery metagenome samples Emma delivered on 20180313 to get an idea of what type of yields we might get from these.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Isolation & Quantification - Geoduck larvae metagenome filter rinses

2018

Miscellaneous

Isolated DNA from two of the geoduck hatchery metagenome samples Emma delivered on 20180313 to get an idea of what type of yields we might get from these.

<<<<<<< HEAD

Performed total alkalinity (TA) titrations on Hollie’s samples using our T5 Excellence titrator (Mettler Toledo) and Rondolino sample changer.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Titrations - Hollie’s Seawater Samples

2018

Miscellaneous

Mar 19, 2018

Performed total alkalinity (TA) titrations on Hollie’s samples using our T5 Excellence titrator (Mettler Toledo) and Rondolino sample changer.

<<<<<<< HEAD

Mar 19, 2018

Performed total alkalinity (TA) titrations on Hollie’s samples using our T5 Excellence titrator (Mettler Toledo) and Rondolino sample changer.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Titrations - Hollie’s Seawater Samples

2018

Miscellaneous

Mar 16, 2018

Performed total alkalinity (TA) titrations on Hollie’s samples using our T5 Excellence titrator (Mettler Toledo) and Rondolino sample changer.

<<<<<<< HEAD

Mar 16, 2018

Received geoduck hatchery metagenome samples from Emma. These samples are intended for DNA isolation.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Samples Received - Geoduck larvae metagenome filter rinses

2018

Samples Received

Mar 13, 2018

Received geoduck hatchery metagenome samples from Emma. These samples are intended for DNA isolation.

<<<<<<< HEAD

Mar 13, 2018

Steven came across a 2012 paper in BMC Bioinformatics (“Exploiting sparseness in de novo genome assembly”) that utilized an assembly program we hadn’t previously encountered: …

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Assembly - Geoduck NovaSeq using SparseAssembler (failed)

2018

Geoduck Genome Sequencing

assembly

geoduck

NovaSeq

Panopea generosa

SparseAssembler

Mar 8, 2018

Steven came across a 2012 paper in BMC Bioinformatics (“Exploiting sparseness in de novo genome assembly”) that utilized an assembly program we hadn’t previously encountered: …

<<<<<<< HEAD

Mar 8, 2018

I’ll begin this entry with a TL;DR (becuase it’s definitely a very long read):

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Progress Report - Titrator

2018

CRM

Rondolino

T5 Excellence

titrator

Mar 6, 2018

I’ll begin this entry with a TL;DR (becuase it’s definitely a very long read):

<<<<<<< HEAD

Mar 6, 2018

Due to hardware limitations on the Apple Xserves we have, we can’t use drives >2TB in size. “Bigfish” was set up to be RAID’d and, as such, has three existing HDDs installed.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Ubuntu Installation - Convert Apple Xserve “bigfish” to Ubuntu

2018

Computer Servicing

Due to hardware limitations on the Apple Xserves we have, we can’t use drives >2TB in size. “Bigfish” was set up to be RAID’d and, as such, has three existing HDDs installed.

<<<<<<< HEAD

Installed an additional 1TB SSD and a USB 3.0 PCI card in woodpecker to make it usable for MinION sequencing. An SSD and USB 3.0 ports are just a couple of the hardware…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Hardware Upgrades - USB 3.0 PCI Card and 1TB SSD in Woodpecker

2018

Computer Servicing

Installed an additional 1TB SSD and a USB 3.0 PCI card in woodpecker to make it usable for MinION sequencing. An SSD and USB 3.0 ports are just a couple of the hardware…

<<<<<<< HEAD

Received a bag of Pacific oysters from Nisbet Oyster Company.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Samples Received - Triploid Crassostrea gigas from Nisbet Oyster Company

2018

Samples Received

Received a bag of Pacific oysters from Nisbet Oyster Company.

<<<<<<< HEAD

Well, I continue to struggle to makek progress on assembling the geoduck Illumina NovaSeq data. Granted, there is a ton of data (374GB!!!!), but it’s still frustrating that…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

NovaSeq Assembly - The Struggle is Real - Real Annoying!

2018

Geoduck Genome Sequencing

AllPaths-LG

assembly

geoduck

jr-assembler

meraculous

mox

NovaSeq

Panopea generosa

SOAPdenovo2

Feb 21, 2018

Well, I continue to struggle to makek progress on assembling the geoduck Illumina NovaSeq data. Granted, there is a ton of data (374GB!!!!), but it’s still frustrating that…

<<<<<<< HEAD

Feb 21, 2018

Trying to get the NovaSeq data assembled using SOAPdenovo2 on the Mox HPC node we have and it will not work.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Assembly - Geoduck Illumina NovaSeq SOAPdenovo2 on Mox (FAIL)

2018

Geoduck Genome Sequencing

Feb 19, 2018

Trying to get the NovaSeq data assembled using SOAPdenovo2 on the Mox HPC node we have and it will not work.

<<<<<<< HEAD

Feb 19, 2018

Finished the ethanol precipitation as described in the MethylMiner (Invitrogen) manual which Yaamini had previously initiated: https://yaaminiv.github.io/Virginica-MBDSeq-Day…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Ethanol Precipitation & DNA Quantification - C. virginica MBD DNA from Yaamini

2018

Samples Submitted

Feb 7, 2018

Finished the ethanol precipitation as described in the MethylMiner (Invitrogen) manual which Yaamini had previously initiated: https://yaaminiv.github.io/Virginica-MBDSeq-Day…

<<<<<<< HEAD

Feb 7, 2018

Attempted to use Meraculous to assemble the trimmed geoduck NovaSeq data.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

NovaSeq Assembly - Trimmed Geoduck NovaSeq with Meraculous

2018

Geoduck Genome Sequencing

assembly

geoduck

Illumina

kmer

kmer genie

meraculous

NovaSeq

Panopea generosa

roadrunner

Feb 5, 2018

Attempted to use Meraculous to assemble the trimmed geoduck NovaSeq data.

<<<<<<< HEAD

Feb 5, 2018

I’ve been working on getting our T5 Excellence titrator (Mettler Toledo) with Rondolino sample changer (Mettler Toledo) set up and operational.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Titrator Setup - Functional Methods & Data Exports

2018

Miscellaneous

Feb 1, 2018

I’ve been working on getting our T5 Excellence titrator (Mettler Toledo) with Rondolino sample changer (Mettler Toledo) set up and operational.

<<<<<<< HEAD

Feb 1, 2018

We would like to get an assembly of the geoduck NovaSeq data that Illumina provided us with.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Adapter Trimming and FASTQC - Illumina Geoduck Novaseq Data

2018

Geoduck Genome Sequencing

FASTQC

geoduck

Illumina

multiqc

NovaSeq

Panopea generosa

trim galore

trimming

Jan 25, 2018

We would like to get an assembly of the geoduck NovaSeq data that Illumina provided us with.

<<<<<<< HEAD

Jan 25, 2018

Steven asked me to install Supernova (by 10x Genomics on our Mox node.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Software Install - 10x Genomics Supernova on Mox (Hyak)

2018

10x genomics

bcl2fastq2

hyak

mox

supernova

Jan 22, 2018

Steven asked me to install Supernova (by 10x Genomics on our Mox node.

<<<<<<< HEAD

Jan 22, 2018

Sent Crassostrea virginica samples to Qiagen, as part of the collaboration we have with them for testing their new bisulfite conversion kit on various reduced representation…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Samples Submitted - C. virginica gDNA, MBD, and MspI to Qiagen

2018

Samples Submitted

Sent Crassostrea virginica samples to Qiagen, as part of the collaboration we have with them for testing their new bisulfite conversion kit on various reduced representation…

<<<<<<< HEAD

I ran Quast to compare all of our current Olympia oyster genome assemblies.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Assembly Comparisons – Oly Assemblies Using Quast

2018

Olympia Oyster Genome Sequencing

assembly

jupyter notebook

Olympia oyster

Ostrea lurida

QUAST

I ran Quast to compare all of our current Olympia oyster genome assemblies.

<<<<<<< HEAD

Quantified the two MspI-digested DNA samples for the Qiagen project from earlier today with the Qubit 3.0 (ThermoFisher).

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Quantification - MspI-digested Crassostrea virginica gDNA

2018

Crassostrea virginica

Eastern oyster

Qubit 3.0

Qubit dsDNA BR

Quantified the two MspI-digested DNA samples for the Qiagen project from earlier today with the Qubit 3.0 (ThermoFisher).

<<<<<<< HEAD

The two MspI restriction digestions from earlier today for our project with Qiagen were subjected to phenol:chloroform cleanup and subsequent ethanol precipitations.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Phenol:Chloroform Extractions and EtOH Precipitations - MspI Digestions of C.virginica DNA from Earlier Today

2018

Crassostrea virginica

Eastern oyster

EtOH precipitation

phenol-chloroform cleanup

The two MspI restriction digestions from earlier today for our project with Qiagen were subjected to phenol:chloroform cleanup and subsequent ethanol precipitations.

<<<<<<< HEAD

Digested two 1.5μg aliquots of Crassostrea virginica isolated 20171211, as part of the project we’re doing with Qiagen.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Restriction Digestion - MspI on Crassotrea virginica gDNA

2018

Miscellaneous

Digested two 1.5μg aliquots of Crassostrea virginica isolated 20171211, as part of the project we’re doing with Qiagen.

<<<<<<< HEAD

Quantified Crassostrea virginica MBD-enriched DNA from earlier today for Qiagen project.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Quantification - C.virginica MBD-enriched DNA

2018

Crassostrea virginica

DNA Quantification

Eastern oyster

Qubit 3.0

Qubit dsDNA BR

Quantified Crassostrea virginica MBD-enriched DNA from earlier today for Qiagen project.

<<<<<<< HEAD

Continued MBD enrichment of C.virginica DNA from yesterday for Qiagen project.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

MBD Enrichment – Crassostrea virginica Sheared DNA Day 3

2018

Crassostrea virginica

Eastern oyster

EtOH precipitation

MBD

MBD enrichment

MethylMiner Methylated DNA Enrichment Kit

Continued MBD enrichment of C.virginica DNA from yesterday for Qiagen project.

<<<<<<< HEAD

Continued MBD enrichment for C.virginica and Qiagen project from yesterday.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

MBD Enrichment – Crassostrea virginica Sheared DNA Day 2

2018

Crassostrea virginica

Eastern oyster

MBD

MBD enrichment

MethylMiner Methylated DNA Enrichment Kit

Jan 9, 2018

Continued MBD enrichment for C.virginica and Qiagen project from yesterday.

<<<<<<< HEAD

Jan 9, 2018

As part of a project with Qiagen to have them try out some of our DNA with their newest DNA bisulfite conversion kit, I previously [isolated DNA from Crassotrea virginica (Ea…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

MBD Enrichment - Crassostrea virginica Sheared DNA Day 1

2018

Miscellaneous

Jan 8, 2018

As part of a project with Qiagen to have them try out some of our DNA with their newest DNA bisulfite conversion kit, I previously [isolated DNA from Crassotrea virginica (Ea…

<<<<<<< HEAD

Jan 8, 2018

I figured it’d be prudent to collect some Eastern oyster (Crassotrea virginica) to have around the lab.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Tissue Sampling - Crassostrea virginica Tissues for Archiving

2017

Miscellaneous

I figured it’d be prudent to collect some Eastern oyster (Crassotrea virginica) to have around the lab.

<<<<<<< HEAD

After I finally resolved the installation of PB Jelly on Emu (running Ubuntu 16.04), I’ve had a PB Jelly assembly running for the past two weeks! I’ve gotten tired of…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Software Install - MSMTP For Email Notices of Bash Job Completion on Emu (Ubuntu)

2017

Miscellaneous

After I finally resolved the installation of PB Jelly on Emu (running Ubuntu 16.04), I’ve had a PB Jelly assembly running for the past two weeks! I’ve gotten tired of…

<<<<<<< HEAD

Continuing Illumina’s generous efforts to use our geoduck samples to test out the robustness of their emerging sequencing technologies, they have requested we send them some…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Samples Submitted - Pulverized Geoduck Tissues to Illumina for More 10x Genomics Sequencing

2017

Geoduck Genome Sequencing

Samples Submitted

2017

Geoduck Genome Sequencing

Samples Submitted

Dec 12, 2017

Continuing Illumina’s generous efforts to use our geoduck samples to test out the robustness of their emerging sequencing technologies, they have requested we send them some…

<<<<<<< HEAD

Dec 12, 2017

I transferred 8ug (136uL) of Crassotrea virginica gDNA (isolated earlier today) to two separate 1.7mL snap cap tubes for sonication/shearing.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Sonication & Bioanalzyer - C. virginica gDNA for MeDIP

2017

Miscellaneous

I transferred 8ug (136uL) of Crassotrea virginica gDNA (isolated earlier today) to two separate 1.7mL snap cap tubes for sonication/shearing.

<<<<<<< HEAD

DNA was isolated from a single adult Eastern oyster (Crassostrea virginica) for a pilot project with Qiagen to test their new DNA bisulfite conversion kit. The oyster was…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Isolation & Quantification - Crassostrea virginica Mantle gDNA

2017

Miscellaneous

DNA was isolated from a single adult Eastern oyster (Crassostrea virginica) for a pilot project with Qiagen to test their new DNA bisulfite conversion kit. The oyster was…

<<<<<<< HEAD

After another attempt to fix PB Jelly, I ran it again.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genome Assembly – Olympia Oyster Illumina & PacBio Using PB Jelly w/BGI Scaffold Assembly

2017

Olympia Oyster Genome Sequencing

assembly

Illumina

jupyter notebook

olympia oyster

Ostrea lurida

PacBio

PB Jelly

pbjelly

QUAST

After another attempt to fix PB Jelly, I ran it again.

<<<<<<< HEAD

The last “fix” didn’t fix everything.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Troubleshooting – PB Jelly Install on Emu Continued

2017

Miscellaneous

The last “fix” didn’t fix everything.

<<<<<<< HEAD

Continuing Illumina’s generous efforts to use our geoduck samples to test out the robustness of their emerging sequencing technologies, they have requested we send them some…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Samples Submitted - Geoduck Tissues to Illumina for More 10x Genomics Sequencing

2017

Geoduck Genome Sequencing

Samples Submitted

geoduck

Illumina

Panopea generosa

Continuing Illumina’s generous efforts to use our geoduck samples to test out the robustness of their emerging sequencing technologies, they have requested we send them some…

<<<<<<< HEAD

I previously installed. Despite no error messages being output, I noticed something odd during my quick post-assembly stats check: The PB Jelly numbers were identical to the…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Troubleshooting - PB Jelly Install on Emu

2017

$PATH

blasr

emu

PB Jelly

I previously installed. Despite no error messages being output, I noticed something odd during my quick post-assembly stats check: The PB Jelly numbers were identical to the…

<<<<<<< HEAD

I isolated DNA from the Crassotrea virginica gonad samples sent by Katie Lotterhos using the E.Z.N.A. Mollusc Kit with the following modifications:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Isolation & Quantification - C. virginica Gonad gDNA

2017

Miscellaneous

I isolated DNA from the Crassotrea virginica gonad samples sent by Katie Lotterhos using the E.Z.N.A. Mollusc Kit with the following modifications:

<<<<<<< HEAD

I ran Quast to compare all of our current Olympia oyster genome assemblies.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Assembly Comparison - Oly Assemblies Using Quast

2017

Olympia Oyster Genome Sequencing

assembly

olympia oyster

Ostrea lurida

QUAST

I ran Quast to compare all of our current Olympia oyster genome assemblies.

<<<<<<< HEAD

Yesterday, I ran PB Jelly using Sean’s Platanus assembly, but that didn’t produce an assembly because PB Jelly was expecting gaps in the Illumina reference assembly…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genome Assembly - Olympia Oyster Illumina & PacBio Using PB Jelly w/BGI Scaffold Assembly

2017

Olympia Oyster Genome Sequencing

assembly

BGI

Illumina

jupyter notebook

olympia oyster

Ostrea lurida

PacBio

PB Jelly

Yesterday, I ran PB Jelly using Sean’s Platanus assembly, but that didn’t produce an assembly because PB Jelly was expecting gaps in the Illumina reference assembly…

<<<<<<< HEAD

Sean had previously attempted to run PB Jelly, but ran into some issues running on Hyak, so I decided to try this on Emu.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genome Assembly - Olympia Oyster Illumina & PacBio Using PB Jelly w/Platanus Assembly

2017

Olympia Oyster Genome Sequencing

assembly

Illumina

jupyter notebook

olympia oyster

Ostrea lurida

PacBio

PB Jelly

Sean had previously attempted to run PB Jelly, but ran into some issues running on Hyak, so I decided to try this on Emu.

<<<<<<< HEAD

Pam Jensen stopped by and dropped off Tanner crab (Chionoecetes bairdi) hemolymph samples (~300) stored in RNA Later (Ambion). Samples were stored at 4C.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Samples Received - Tanner Crab Hemolymph in RNA Later from Pam Jensen

2017

Samples Received

Tanner Crab RNAseq

Pam Jensen stopped by and dropped off Tanner crab (Chionoecetes bairdi) hemolymph samples (~300) stored in RNA Later (Ambion). Samples were stored at 4C.

<<<<<<< HEAD

We received three Tanner crab (Chionoecetes bairdi)hemolymph samples from Pam Jensen (NOAA) yesterday. From her email to Steven:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation & Quantification - Tanner crab hemolymph

2017

Tanner Crab RNAseq

Nov 7, 2017

We received three Tanner crab (Chionoecetes bairdi)hemolymph samples from Pam Jensen (NOAA) yesterday. From her email to Steven:

<<<<<<< HEAD

Nov 7, 2017

List of software that needed installing to run ALPACA:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Software Installation - ALPACA on Roadrunner

2017

Miscellaneous

List of software that needed installing to run ALPACA:

<<<<<<< HEAD

Ah, the joys of bioinformatics. I just received an email from Mox indicating that [the Masurca assembly I started 11 DAYS AGO…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Software Crash - Olympia oyster genome assembly with Masurca on Mox

2017

Miscellaneous

Ah, the joys of bioinformatics. I just received an email from Mox indicating that [the Masurca assembly I started 11 DAYS AGO…

<<<<<<< HEAD

I followed along with what Sean previously did when installing on Emu, but it appears he didn’t install it in the shared location to make it accessible to all users. So, I’m…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Software Installation - PB Jelly Suite and Blasr on Emu

2017

blasr

emu

PacBio

pbjelly

Oct 30, 2017

I followed along with what Sean previously did when installing on Emu, but it appears he didn’t install it in the shared location to make it accessible to all users. So, I’m…

<<<<<<< HEAD

Oct 30, 2017

Had problems with Docker and Jupyter Notebook inexplicably dying and deleting all the files in the working directory of the Jupyter Notebook (which also happened to be the…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genome Assembly - Olympia oyster Illumina & PacBio Reads Using Redundans

2017

Olympia Oyster Genome Sequencing

Oct 24, 2017

Had problems with Docker and Jupyter Notebook inexplicably dying and deleting all the files in the working directory of the Jupyter Notebook (which also happened to be the…

<<<<<<< HEAD

Oct 24, 2017

I recently finished an assembly of our Olympia oyster PacBio data using Canu and thought it would be interesting to compare to Sean’s Canu assembly.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Assembly Comparison - Oly PacBio Canu: Sam vs. Sean with Quast

2017

I recently finished an assembly of our Olympia oyster PacBio data using Canu and thought it would be interesting to compare to Sean’s Canu assembly.

<<<<<<< HEAD

Uh oh. There appears to be some data that’s been removed from Owl. I noticed this earlier when trying to look at some of Sean’s data. His data should be in a folder with his…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

FAIL - Missing Data on Owl!

2017

fail

Uh oh. There appears to be some data that’s been removed from Owl. I noticed this earlier when trying to look at some of Sean’s data. His data should be in a folder with his…

<<<<<<< HEAD

Saw this tweet this morning and thought this would be good to try out for our Olympia oyster genome assemblies, as it will handle “hybrid” assemblies (i.e. short-reads and…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genome Assembly - Olympia oyster Illumina & PacBio reads using MaSuRCA

2017

Olympia Oyster Genome Sequencing

<<<<<<< HEAD

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Software Installation - MaSuRCA v3.2.3 Assembler on Mox (Hyak)

2017

Miscellaneous

Oct 19, 2017

Saw this tweet this morning and thought this would be good to try out for our Olympia oyster genome assemblies, as it will handle “hybrid” assemblies (i.e. short-reads and…

<<<<<<< HEAD

Oct 19, 2017

Uh, not sure what happened here:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Fail - Directory Contents Deleted!

2017

Miscellaneous

Uh, not sure what happened here:

<<<<<<< HEAD

I decided to run Canu myself, since documentation for Sean’s Canu run is a bit lacking. Additionally, it looks like he specified a genome size of 500Mbp, which is probably…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genome Assembly - Olympia oyster PacBio Canu v1.6

2017

Olympia Oyster Genome Sequencing

canu

jupyter notebook

olympia oyster

Ostrea lurida

PacBio

I decided to run Canu myself, since documentation for Sean’s Canu run is a bit lacking. Additionally, it looks like he specified a genome size of 500Mbp, which is probably…

<<<<<<< HEAD

After working with all of this Olympia oyster genome sequencing data, I remembered that we had an old, singular PacBio SMRT cell file (from June 2013). This file didn’t seem…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Management - Convert Oly PacBio H5 to FASTQ

2017

Olympia Oyster Genome Sequencing

FASTQ

olympia oyster

Ostrea lurida

PacBio

Oct 9, 2017

After working with all of this Olympia oyster genome sequencing data, I remembered that we had an old, singular PacBio SMRT cell file (from June 2013). This file didn’t seem…

<<<<<<< HEAD

Oct 9, 2017

Decided to compare the Redundans using Canu as reference and Redundans using Racon as reference. Both reference assemblies were just our PacBio data.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genome Assembly - Olympia oyster Redundans/Canu vs. Redundans/Racon

2017

Olympia Oyster Genome Sequencing

Oct 6, 2017

Decided to compare the Redundans using Canu as reference and Redundans using Racon as reference. Both reference assemblies were just our PacBio data.

<<<<<<< HEAD

Oct 6, 2017

Redundans should assemble both Illumina and PacBio data, so let’s do that.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genome Assembly - Olympia Oyster Redundans with Illumina + PacBio

2017

Olympia Oyster Genome Sequencing

Oct 5, 2017

Redundans should assemble both Illumina and PacBio data, so let’s do that.

<<<<<<< HEAD

Oct 5, 2017

Previously, I used the following three tools to do quick assembly of our Olympia oyster PacBio data:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genome Assembly - minimap/miniasm/racon Overview

2017

Olympia Oyster Genome Sequencing

Oct 4, 2017

Previously, I used the following three tools to do quick assembly of our Olympia oyster PacBio data:

<<<<<<< HEAD

Oct 4, 2017

Having run through this a bunch of times now, I realized that the analysis below incorrectly identifies the outputs from Sean’s Redundans runs. The correct output from each…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Assembly Comparisons - Olympia oyster genome assemblies

2017

Olympia Oyster Genome Sequencing

docker

jupyter notebook

olympia oyster

Ostrea lurida

QUAST

Having run through this a bunch of times now, I realized that the analysis below incorrectly identifies the outputs from Sean’s Redundans runs. The correct output from each…

<<<<<<< HEAD

Received and stored @-80C in rack 8, row 5, column 5.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Samples Received - C.virginica gonad tissue from Katie Lotterhos

2017

Samples Received

Received and stored @-80C in rack 8, row 5, column 5.

<<<<<<< HEAD

I guess one of my primary goals is to make sure I actually write my monthly goals each month.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Goals - October 2017

2017

Goals

Oct 2, 2017

I guess one of my primary goals is to make sure I actually write my monthly goals each month.

<<<<<<< HEAD

Oct 2, 2017

In this GitHub Issue, Steven had suggested I try out the minimap/miniasm/racon pipeline for assembling our Olympia oyster PacBio data.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genome Assembly - Olympia oyster PacBio minimap/miniasm/racon

2017

minimap

racon

miniasm

olympia oyster

Ostrea lurida

PacBio

In this GitHub Issue, Steven had suggested I try out the minimap/miniasm/racon pipeline for assembling our Olympia oyster PacBio data.

<<<<<<< HEAD

In this GitHub Issue, Steven had suggested I try out the minimap/miniasm/racon pipeline for assembling our Olympia oyster PacBio data.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genome Assembly - Olympia oyster PacBio minimap/miniasm/racon

2017

Olympia Oyster Genome Sequencing

jupyter notebook

miniasm

olympia oyster

Ostrea lurida

PacBio

racon

In this GitHub Issue, Steven had suggested I try out the minimap/miniasm/racon pipeline for assembling our Olympia oyster PacBio data.

<<<<<<< HEAD

In this GitHub Issue, Steven had suggested I try out the minimap/miniasm/racon pipeline for assembling our Olympia oyster PacBio data.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genome Assembly - Olympia oyster PacBio minimap/miniasm/racon

2017

Olympia Oyster Genome Sequencing

jupyter notebook

minimap

olympia oyster

Ostrea lurida

PacBio

Sep 7, 2017

In this GitHub Issue, Steven had suggested I try out the minimap/miniasm/racon pipeline for assembling our Olympia oyster PacBio data.

<<<<<<< HEAD

Sep 7, 2017

Continuing Illumina’s generous efforts to use our geoduck samples to test out the robustness of their emerging sequencing technologies, they have requested we send them some…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Samples Submitted - Geoduck Ctenidia to Illumina for 10x Genomics Sequencing

2017

Geoduck Genome Sequencing

Samples Submitted

10x genomics

ctenidia

geoduck

Illumina

Panopea generosa

Continuing Illumina’s generous efforts to use our geoduck samples to test out the robustness of their emerging sequencing technologies, they have requested we send them some…

<<<<<<< HEAD

Here’s a brief overview of what Sean has done with the Oly genome assembly front.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Project Progress - Olympia Oyster Genome Assemblies by Sean Bennett

2017

Olympia Oyster Genome Sequencing

BGI

Illumina

olympia oyster

Ostrea lurida

PacBio

Here’s a brief overview of what Sean has done with the Oly genome assembly front.

<<<<<<< HEAD

The HDD we received from Illumina last week only had data (i.e. fastq files) from the NovaSeq runs they performed - nothing from either the MiSeq, nor the HiSeq runs.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Management - Illumina Geoduck HiSeq & MiSeq Data

2017

Geoduck Genome Sequencing

Aug 8, 2017

The HDD we received from Illumina last week only had data (i.e. fastq files) from the NovaSeq runs they performed - nothing from either the MiSeq, nor the HiSeq runs.

<<<<<<< HEAD

Aug 8, 2017

Data, data, data! That is the theme for this month.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Goals - August 2017

2017

Goals

Aug 3, 2017

Data, data, data! That is the theme for this month.

<<<<<<< HEAD

Aug 3, 2017

We previously sent some geoduck samples to Illumina, as part of a pilot project for them to test out a new sequencing platform. The data has finally arrived!

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Received - Geoduck Genome Sequencing by Illumina

2017

Geoduck Genome Sequencing

Jul 31, 2017

We previously sent some geoduck samples to Illumina, as part of a pilot project for them to test out a new sequencing platform. The data has finally arrived!

<<<<<<< HEAD

Jul 31, 2017

Sent the following RNA to Katherine Silliman at the Univ. of Chicago for RNAseq. All RNA was isolated on 20170719, except SN-10-16, which was isolated on 20170710.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Sample Submission - Olympia oyster gonad RNA to Katherine Silliman @ Univ. of Chicago

2017

Samples Submitted

NF-10 22

NF-10-23

NF-10-24

NF-10-26

NF-10-28

NF-10-30

olympia oyster

Ostrea lurida

RNA

SN-10-16

SN-10-17

SN-10-20

SN-10-25

SN-10-26

SN-10-31

Jul 20, 2017

Sent the following RNA to Katherine Silliman at the Univ. of Chicago for RNAseq. All RNA was isolated on 20170719, except SN-10-16, which was isolated on 20170710.

<<<<<<< HEAD

Jul 20, 2017

My previous go at this was a little premature - I didn’t wait for Laura to fully annotate her slides/blocks. Little did I know, the tissue was mostly visceral mass and, as…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation - Olympia oyster gonad tissue in paraffin histology blocks

2017

Miscellaneous

Jul 19, 2017

My previous go at this was a little premature - I didn’t wait for Laura to fully annotate her slides/blocks. Little did I know, the tissue was mostly visceral mass and, as…

<<<<<<< HEAD

Jul 19, 2017

UPDATE 20170712: The RNA I isolated below is from incorrect regions of tissue. I misunderstood exactly what this tissue was, and admittedly, jumped the gun. The tissue is…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation - Olympia oyster gonad tissue in paraffin histology blocks

2017

Miscellaneous

Jul 10, 2017

UPDATE 20170712: The RNA I isolated below is from incorrect regions of tissue. I misunderstood exactly what this tissue was, and admittedly, jumped the gun. The tissue is…

<<<<<<< HEAD

Jul 10, 2017

Submitted the FASTQ files from the UW PacBio Data from 20170323 to the [NCBI sequence read archive (SRA)(https://www.ncbi.nlm.nih.gov/sra).

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Management - SRA Submission Olympia Oyster UW PacBio Data from 20170323

2017

Olympia Oyster Genome Sequencing

Submitted the FASTQ files from the UW PacBio Data from 20170323 to the [NCBI sequence read archive (SRA)(https://www.ncbi.nlm.nih.gov/sra).

<<<<<<< HEAD

I’d previously attempted to archive this data set on multiple occasions, across multiple days, but network dropouts kept killing my connection to the server (Owl) and, in…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Management – Tarball of Olympia oyster UW PacBio Data from 20170323

2017

Olympia Oyster Genome Sequencing

I’d previously attempted to archive this data set on multiple occasions, across multiple days, but network dropouts kept killing my connection to the server (Owl) and, in…

<<<<<<< HEAD

Added UW PacBio FASTQ files to our nightingales Google Sheet for keeping track of our high-throughput sequencing projects.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Management - OLYMPIA OYSTER UW PACBIO DATA (FROM 20170323) TO NIGHTINGALES

2017

Olympia Oyster Genome Sequencing

Added UW PacBio FASTQ files to our nightingales Google Sheet for keeping track of our high-throughput sequencing projects.

<<<<<<< HEAD

I’ve been asked to isolate RNA from some paraffin-embedded Olympia oyster gonad tissue.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Sample Annotation - Olympia oyster histology blocks (from Laura Spencer)

2017

Miscellaneous

I’ve been asked to isolate RNA from some paraffin-embedded Olympia oyster gonad tissue.

<<<<<<< HEAD

Last August, we made our initial submission of this paper to PeeJ.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Manuscript Re-submission - Oly Stress Response to PeerJ for Review

2017

Miscellaneous

Last August, we made our initial submission of this paper to PeeJ.

<<<<<<< HEAD

Due to other priorities, getting this PacBio data sorted and prepped for our [next gen sequencing data management plan (DMP)]…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Management - Olympia oyster UW PacBio Data from 20170323

2017

Olympia Oyster Genome Sequencing

jupyter notebook

olympia oyster

Ostrea lurida

PacBio

Due to other priorities, getting this PacBio data sorted and prepped for our [next gen sequencing data management plan (DMP)]…

<<<<<<< HEAD

Updated a couple of GitHub Wikis:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

GitHub Curation

2017

Miscellaneous

Jun 22, 2017

Updated a couple of GitHub Wikis:

<<<<<<< HEAD

Jun 22, 2017

Well, my previous goal was to tidy up an existing manuscript and get it re-submitted to PeerJ. That’s pretty much done, as Steven will be giving a final once over and…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Goals - June 2017

2017

Goals

Jun 1, 2017

Well, my previous goal was to tidy up an existing manuscript and get it re-submitted to PeerJ. That’s pretty much done, as Steven will be giving a final once over and…

<<<<<<< HEAD

Jun 1, 2017

Used the MethylFlash Methylated DNA Quantification Kit (Colorimetric) from Epigentek to quantify methylation in these coral DNA samples.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Methylation Quantification - Acropora cervicornis (Staghorn coral) DNA from Javier Casariego (FIU)

2017

Miscellaneous

Used the MethylFlash Methylated DNA Quantification Kit (Colorimetric) from Epigentek to quantify methylation in these coral DNA samples.

<<<<<<< HEAD

I quantified the three samples (listed below) that I SpeedVac’d yesterday using the the Roberts Lab Qubit 3.0.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Quantification - Acropora cervicornis (Staghorn coral) DNA from Javier Casariego (FIU)

2017

Miscellaneous

I quantified the three samples (listed below) that I SpeedVac’d yesterday using the the Roberts Lab Qubit 3.0.

<<<<<<< HEAD

Three samples (of the 62 total) that were quantified earlier today, had concentrations too low for use in the methylation assay:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Concentration - Acropora cervicornis (Staghorn coral) DNA from Javier Casariego (FIU)

2017

Miscellaneous

Three samples (of the 62 total) that were quantified earlier today, had concentrations too low for use in the methylation assay:

<<<<<<< HEAD

DNA samples received yesterday were quantified using the Roberts Lab Qubit 3.0 to improve quantification accuracy (samples provided by Javier were quantified via NanoDrop…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Quantification - Acropora cervicornis (Staghorn coral) DNA from Javier Casariego (FIU)

2017

Miscellaneous

DNA samples received yesterday were quantified using the Roberts Lab Qubit 3.0 to improve quantification accuracy (samples provided by Javier were quantified via NanoDrop…

<<<<<<< HEAD

Received histology blocks and slides for Laura Spencer.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Samples Received - Olympia oyster Histology Blocks and Slides (for Laura Spencer)

2017

Samples Received

Received histology blocks and slides for Laura Spencer.

<<<<<<< HEAD

Received 62 coral (Acropora cervicornis) DNA samples from Javier Casariego at FIU.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Samples Received - Acropora cervicornis (Staghorn coral) DNA from Javier Casariego (FIU)

2017

Samples Received

Received 62 coral (Acropora cervicornis) DNA samples from Javier Casariego at FIU.

<<<<<<< HEAD

A day late, but definitely not a dollar short!

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Goals - May 2017

2017

Goals

May 2, 2017

A day late, but definitely not a dollar short!

<<<<<<< HEAD

May 2, 2017

(http://eagle.fish.washington.edu/Arabidopsis/20170419_Overleaf_sci_data_oly_gbs_submission.png)

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Manuscript Writing - Submitted!

2017

Genotype-by-sequencing at BGI

Apr 19, 2017

(http://eagle.fish.washington.edu/Arabidopsis/20170419_Overleaf_sci_data_oly_gbs_submission.png)

<<<<<<< HEAD

Apr 19, 2017

For Pub-a-thon 2017, Steven has asked us to put together a 14 day plan for our manuscripts.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Manuscript - Oly GBS 14 Day Plan

2017

Genotype-by-sequencing at BGI

Apr 18, 2017

For Pub-a-thon 2017, Steven has asked us to put together a 14 day plan for our manuscripts.

<<<<<<< HEAD

Apr 18, 2017

Back in December 2016, we sent off Ostrea lurida DNA to the UW PacBio sequencing facility. This is an attempt to fill in the gaps left from the BGI genome sequencing project.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Received - Olympia oyster PacBio Data

2017

Olympia Oyster Genome Sequencing

Mar 23, 2017

Back in December 2016, we sent off Ostrea lurida DNA to the UW PacBio sequencing facility. This is an attempt to fill in the gaps left from the BGI genome sequencing project.

<<<<<<< HEAD

Mar 23, 2017

An earlier attempt at submitting these files failed.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Management – SRA Submission Oly GBS Batch Submission

2017

Genotype-by-sequencing at BGI

An earlier attempt at submitting these files failed.

<<<<<<< HEAD

Heard back from Synology and they indicated I should click the “Repair” option to fix the System Partition Failed error message seen previously.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Computing - Owl Partially Restored

2017

Computer Servicing

Heard back from Synology and they indicated I should click the “Repair” option to fix the System Partition Failed error message seen previously.

<<<<<<< HEAD

[I had previously submitted the two non-demultiplexed genotype-by-sequencing (GBS) files provided by BGI to the NCBI short read archive…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Management - SRA Submission Oly GBS Batch Submission Fail

2017

Genotype-by-sequencing at BGI

Mar 20, 2017

[I had previously submitted the two non-demultiplexed genotype-by-sequencing (GBS) files provided by BGI to the NCBI short read archive…

<<<<<<< HEAD

Mar 20, 2017

TL;DR - Server didn’t recover after firmware update last night. “Repair” is an option listed in the web interface, but I want to confirm with Synology what will happen…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Troubleshooting - Synology NAS (Owl) Down After Update

2017

Computer Servicing

Mar 18, 2017

TL;DR - Server didn’t recover after firmware update last night. “Repair” is an option listed in the web interface, but I want to confirm with Synology what will happen…

<<<<<<< HEAD

Mar 18, 2017

OK, so things have improved since the last attempt at getting this BGI script to run and demultiplex the raw data.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Computing – Oly BGI GBS Reproducibility; fail?

2017

Genotype-by-sequencing at BGI

BGI

GBS

genotype-by-sequencing

jupyter notebook

olympia oyster

Ostrea lurida

Mar 17, 2017

OK, so things have improved since the last attempt at getting this BGI script to run and demultiplex the raw data.

<<<<<<< HEAD

Mar 17, 2017

Well, my previous attempt at reproducing the demultiplexing that BGI performed was an exercise in futility. BGI got back to me with the following message:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Computing – Oly BGI GBS Reproducibility Fail (but, less so than last time)…

2017

BS-seq Libraries for Sequencing at Genewiz

Mar 14, 2017

Well, my previous attempt at reproducing the demultiplexing that BGI performed was an exercise in futility. BGI got back to me with the following message:

<<<<<<< HEAD

Mar 14, 2017

Since we’re preparing a manuscript that relies on BGI’s manipulation/handling of the genotype-by-sequencing data, I attempted to could reproduce the demultiplexing steps…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Computing - Oly BGI GBS Reproducibility Fail

2017

Genotype-by-sequencing at BGI

BGI

GBS

genotype-by-sequencing

iTools

olympia oyster

Ostrea lurida

Since we’re preparing a manuscript that relies on BGI’s manipulation/handling of the genotype-by-sequencing data, I attempted to could reproduce the demultiplexing steps…

<<<<<<< HEAD

Last week, I ran the two raw FASTQ files through FastQC. As expected, FastQC detected “errors”. These errors are due to the presence of adapter sequences, barcodes, and the…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

FASTQC - Oly BGI GBS Raw Illumina Data Demultiplexed

2017

Genotype-by-sequencing at BGI

BGI

docker

FASTQC

GBS

genotype-by-sequencing

jupyter notebook

olympia oyster

Ostrea lurida

ostrich

Last week, I ran the two raw FASTQ files through FastQC. As expected, FastQC detected “errors”. These errors are due to the presence of adapter sequences, barcodes, and the…

<<<<<<< HEAD

Below, is the Jupyter notebook I used to run the FastQC analysis on the two files. I’ve embedded for quick viewing, but it might be easier to view the notebook via the…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

FASTQC - Oly BGI GBS Raw Illumina Data

2017

Genotype-by-sequencing at BGI

BGI

FASTQC

GBS

genotype-by-sequencing

jupyter notebook

olympia oyster

Ostrea lurida

Mar 2, 2017

Below, is the Jupyter notebook I used to run the FastQC analysis on the two files. I’ve embedded for quick viewing, but it might be easier to view the notebook via the…

<<<<<<< HEAD

Mar 2, 2017

Oh, actually, there is another, smaller goal that will be very difficult to achieve: win Pub-a-Thon. Jay’s taken a massive lead and has a nearly complete manuscript ready…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Goals - March 2017

2017

Goals

Mar 1, 2017

Oh, actually, there is another, smaller goal that will be very difficult to achieve: win Pub-a-Thon. Jay’s taken a massive lead and has a nearly complete manuscript ready…

<<<<<<< HEAD

Mar 1, 2017

I previously highlighted some of the issues I was having using Authorea.com as an writing platform.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Manuscript Writing - More “Nuances” Using Authorea

2017

Miscellaneous

Feb 28, 2017

I previously highlighted some of the issues I was having using Authorea.com as an writing platform.

<<<<<<< HEAD

Feb 28, 2017

Jay received notice from UC Berkeley that the sequencing data from his coral RADseq was ready. In addition, the sequencing contains some epiRADseq data from samples provided…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Received - Jay’s Coral RADseq and Hollie’s Geoduck Epi-RADseq

2017

Anthopleura elegantissima

docker

geoduck

jupyter notebook

Feb 27, 2017

Jay received notice from UC Berkeley that the sequencing data from his coral RADseq was ready. In addition, the sequencing contains some epiRADseq data from samples provided…

<<<<<<< HEAD

Feb 27, 2017

Prepared a short read archive (SRA) submission for archiving our Olympia oyster genotype-by-sequencing (GBS) data in NCBI. This is in preparation for submission of the mansuc…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Management - SRA Submission of Ostrea lurida GBS FASTQ Files

2017

Genotype-by-sequencing at BGI

SRA Submissions

Feb 8, 2017

Prepared a short read archive (SRA) submission for archiving our Olympia oyster genotype-by-sequencing (GBS) data in NCBI. This is in preparation for submission of the mansuc…

<<<<<<< HEAD

Feb 8, 2017

First goal is to be the first person in lab to post their goals each month. Props to one of our new grad students, Yaamini Venkataraman on beating me this month!

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Goals - February 2017

2017

Goals

Feb 2, 2017

First goal is to be the first person in lab to post their goals each month. Props to one of our new grad students, Yaamini Venkataraman on beating me this month!

<<<<<<< HEAD

Feb 2, 2017

PROBLEM: Authorea spits out a browser-crashing “unresponsive script” message (actually, lots and lots of them; clicking “Stop script” or “Continue” just results in…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Manuscript Writing - The “Nuances” of Using Authorea

2017

Genotype-by-sequencing at BGI

Miscellaneous

Jan 23, 2017

PROBLEM: Authorea spits out a browser-crashing “unresponsive script” message (actually, lots and lots of them; clicking “Stop script” or “Continue” just results in…

<<<<<<< HEAD

Jan 23, 2017

Sent 10μg of the geoduck gDNA I isolated earlier today to Illumina on dry ice via FedEx Standard Overnight service.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Sample Submission – Geoduck gDNA for Illumina Pilot Sequencing Project

2017

Geoduck Genome Sequencing

Samples Submitted

Sent 10μg of the geoduck gDNA I isolated earlier today to Illumina on dry ice via FedEx Standard Overnight service.

<<<<<<< HEAD

We were previously approached by Cindy Lawley (Illumina Market Development) for possible participation in an Illumina product development project, in which they wanted to…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Isolation - Geoduck gDNA for Illumina-initiated Sequencing Project

2017

Geoduck Genome Sequencing

DNA Isolation

DNA Quantification

E.Z.N.A. Mollusc Kit

gDNA

gel

geoduck

Illumina

Panopea generosa

Qubit 3.0

Qubit dsDNA BR

We were previously approached by Cindy Lawley (Illumina Market Development) for possible participation in an Illumina product development project, in which they wanted to…

<<<<<<< HEAD

Previously, Sean and Steven identified two potentially corrupt FASTQ files. I contacted BGI about getting replacement files and they informed me that all versions of the…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Management - Replacement of Corrupt BGI Oly Genome FASTQ Files

2017

Olympia Oyster Genome Sequencing

BGI

jupyter notebook

md5

olympia oyster

Ostrea lurida

Jan 4, 2017

Previously, Sean and Steven identified two potentially corrupt FASTQ files. I contacted BGI about getting replacement files and they informed me that all versions of the…

<<<<<<< HEAD

Jan 4, 2017

One of the long-running goals I’ve had is to get this Oly GBS data taken care of and out the door to publication. I think I will finally succeed with this, with the help of P…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Goals - January 2017

2017

Goals

Jan 3, 2017

One of the long-running goals I’ve had is to get this Oly GBS data taken care of and out the door to publication. I think I will finally succeed with this, with the help of P…

<<<<<<< HEAD

Jan 3, 2017

Yesterday, I downloaded the Illumina FASTQ files provided by Genewiz for Hollie Putnam’s reduced representation bisulfite geoduck libraries. However, Genewiz had not…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Management - Geoduck RRBS Data Integrity Verification

2016

geoduck

jupyter notebook

md5

Panopea generosa

RRBS

Dec 30, 2016

Yesterday, I downloaded the Illumina FASTQ files provided by Genewiz for Hollie Putnam’s reduced representation bisulfite geoduck libraries. However, Genewiz had not…

<<<<<<< HEAD

Dec 30, 2016

Hollie Putnam prepared some reduced representation bisulfite Illumina libraries and had them sequenced by Genewiz.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Received - Geoduck RRBS Sequencing Data

2016

Genewiz

geoduck

Illumina

Panopea generosa

RRBS

Dec 29, 2016

Hollie Putnam prepared some reduced representation bisulfite Illumina libraries and had them sequenced by Genewiz.

<<<<<<< HEAD

Dec 29, 2016

Sent the following samples to Illumina for possible selection in a new pilot sequencing platform they’re working on.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Sample Submission - Geoduck Tissue & gDNA for Illumina Pilot Sequencing Project

2016

Geoduck Genome Sequencing

Samples Submitted

geoduck

Illumina

Panopea generosa

Dec 21, 2016

Sent the following samples to Illumina for possible selection in a new pilot sequencing platform they’re working on.

<<<<<<< HEAD

Dec 21, 2016

We were approached by Cindy Lawley (Illumina Market Development) yesterday to see if we’d be able to participate in some product development. We agreed and need some geoduck…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Isolation - Geoduck gDNA for Potential Illumina-initiated Sequencing Project

2016

Geoduck Genome Sequencing

DNA Isolation

E.Z.N.A. Mollusc Kit

gel

geoduck

O'geneRuler DNA Ladder Mix

Panopea generosa

Qubit 3.0

Qubit dsDNA BR

`Dec 21, 2016`{=html}

Hollie Putnam asked me to help her get samples ready for submission for Illumina sequencing at Genewiz.

<<<<<<< HEAD

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Sample Submission - Geoduck Reduced Representation Bisulfite Pooled Libraries

2016

Samples Submitted

geoduck

Hollie Putnam

Panopea generosa

RRBS

Dec 20, 2016

Hollie Putnam asked me to help her get samples ready for submission for Illumina sequencing at Genewiz.

<<<<<<< HEAD

Dec 20, 2016

Submitted 10μg (30.7μL) of the O.lurida gDNA I isolated on 20161214 to the UW PacBio facility - Order #450.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Sample Submission - Ostrea lurida gDNA for PacBio Sequencing

2016

Olympia Oyster Genome Sequencing

Samples Submitted

gDNA

olympia oyster

Ostrea lurida

PacBio

Dec 19, 2016

Submitted 10μg (30.7μL) of the O.lurida gDNA I isolated on 20161214 to the UW PacBio facility - Order #450.

<<<<<<< HEAD

Dec 19, 2016

After completing the downloads of these files from BGI, I needed to verify that the downloaded copies matched the originals. Below is a Jupyter Notebook detailing how I…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Management - Integrity Check of Final BGI Olympia Oyster & Geoduck Data

2016

Geoduck Genome Sequencing

Olympia Oyster Genome Sequencing

Dec 15, 2016

After completing the downloads of these files from BGI, I needed to verify that the downloaded copies matched the originals. Below is a Jupyter Notebook detailing how I…

<<<<<<< HEAD

Dec 15, 2016

In an attempt to improve upon the partial genome assembly we received from BGI, we will be sending DNA to the UW PacBio core facility for additional sequencing.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Isolation - Ostrea lurida DNA for PacBio Sequencing

2016

Olympia Oyster Genome Sequencing

DNA Isolation

DNA Quantification

E.Z.N.A. Mollusc Kit

gDNA

gel

olympia oyster

Ostrea lurida

Qubit 3.0

Qubit dsDNA BR

In an attempt to improve upon the partial genome assembly we received from BGI, we will be sending DNA to the UW PacBio core facility for additional sequencing.

<<<<<<< HEAD

Last week I downloaded the final BGI data files and assemblies for Olympia oyster and geoduck genome sequencing projects. However, the output from the download command made…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Management - Trim Output Cells from Jupyter Notebook

2016

jupyter notebook

Last week I downloaded the final BGI data files and assemblies for Olympia oyster and geoduck genome sequencing projects. However, the output from the download command made…

<<<<<<< HEAD

We received info to download the final data and genome assembly files for geoduck and Olympia oyster from BGI.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Management - Download Final BGI Genome & Assembly Files

2016

Geoduck Genome Sequencing

Olympia Oyster Genome Sequencing

BGI

geoduck

jupyter notebook

olympia oyster

Ostrea lurida

owl

Panopea generosa

We received info to download the final data and genome assembly files for geoduck and Olympia oyster from BGI.

<<<<<<< HEAD

Well, I’ve finally progressed with the Olly GBS analysis!

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Goals - December 2016

2016

Goals

Well, I’ve finally progressed with the Olly GBS analysis!

<<<<<<< HEAD

Continued the analysis I started the other day. Still following Katherine Silliman’s notebook for guidance.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Analysis - Continued O.lurida Fst Analysis from GBS Data

2016

Genotype-by-sequencing at BGI

Olympia oyster reciprocal transplant

Continued the analysis I started the other day. Still following Katherine Silliman’s notebook for guidance.

<<<<<<< HEAD

Trying to continue my Oly GBS analsyis from the other day and follow along with Katherine Silliman’s notebook

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Computing - An Excercise in Futility

2016

jupyter notebook

Nov 30, 2016

Trying to continue my Oly GBS analsyis from the other day and follow along with Katherine Silliman’s notebook

<<<<<<< HEAD

Nov 30, 2016

Finally running some analysis on the output from my PyRad analysison 20160727.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Analysis - Initial O.lurida Fst Determination from GBS Data

2016

Genotype-by-sequencing at BGI

Olympia oyster reciprocal transplant

docker

dockerfile

FST

jupyter notebook

olympia oyster

Ostrea lurida

vcftools

Finally running some analysis on the output from my PyRad analysison 20160727.

<<<<<<< HEAD

UPDATE 20170104 - These two corrupt files have been replaced with non-corrupt files.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Management - Tracking O.lurida FASTQ File Corruption

2016

Olympia Oyster Genome Sequencing

UPDATE 20170104 - These two corrupt files have been replaced with non-corrupt files.

<<<<<<< HEAD

Sean got the remaining Xserves configured to run independently from the master node of the cluster they belonged to and installed OS X 10.11 (El Capitan).

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Computer Management - Additional Configurations for Reformatted Xserves

2016

Computer Servicing

Nov 16, 2016

Sean got the remaining Xserves configured to run independently from the master node of the cluster they belonged to and installed OS X 10.11 (El Capitan).

<<<<<<< HEAD

Nov 16, 2016

Re-examining our backup options for our two Synology servers (Eagle & Owl), I realized that they were both backing up to the just my account on UW’s unlimited Google Drive…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Management - Modify Eagle/Owl Cloud Sync Account

2016

Computer Servicing

Nov 7, 2016

Re-examining our backup options for our two Synology servers (Eagle & Owl), I realized that they were both backing up to the just my account on UW’s unlimited Google Drive…

<<<<<<< HEAD

Nov 7, 2016

I had an existing instance that still had data on it from my PyRad analysis on 20160727 that I needed to retrieve.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Computing - Retrieve data from Amazon EC2 Instance

2016

Genotype-by-sequencing at BGI

Olympia oyster reciprocal transplant

Nov 4, 2016

I had an existing instance that still had data on it from my PyRad analysis on 20160727 that I needed to retrieve.

<<<<<<< HEAD

Nov 4, 2016

Well, I’m serious this time. My goal for this month is to complete the Oly GBS data analysis and, get the data sets and data analysis prepared/placed in satisfactory…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Goals - November 2016

2016

Goals

Nov 2, 2016

Well, I’m serious this time. My goal for this month is to complete the Oly GBS data analysis and, get the data sets and data analysis prepared/placed in satisfactory…

<<<<<<< HEAD

Nov 2, 2016

Received another set of Panopea generosa genome assembly data from BGI back in May! I neglected to create MD5 checksums, as well as a readme file for this data set! Of…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Management – Geoduck Small Insert Library Genome Assembly from BGI

2016

Geoduck Genome Sequencing

BGI

geoduck

jupyter notebook

Panopea generosa

Oct 25, 2016

Received another set of Panopea generosa genome assembly data from BGI back in May! I neglected to create MD5 checksums, as well as a readme file for this data set! Of…

<<<<<<< HEAD

Oct 25, 2016

Last month’s goals, as it turns out, were way too ambitious. This month’s goal will be to get the Oly GBS data analysis fully completed (currently have individuals data, but…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Goals - October 2016

2016

Goals

Oct 3, 2016

Last month’s goals, as it turns out, were way too ambitious. This month’s goal will be to get the Oly GBS data analysis fully completed (currently have individuals data, but…

<<<<<<< HEAD

Oct 3, 2016

Previously downloaded Jay’s epiRADseq data that was provided by the Genomic Sequencing Laboratory at UC-Berkeley. It was provided already demultiplexed (which is very nice…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Received – Jay’s Coral epiRADseq - Not Demultiplexed

2016

Miscellaneous

Sep 19, 2016

Previously downloaded Jay’s epiRADseq data that was provided by the Genomic Sequencing Laboratory at UC-Berkeley. It was provided already demultiplexed (which is very nice…

<<<<<<< HEAD

Sep 19, 2016

I helped Katherine Silliman with her oyster sampling today from her ocean acidification experiment with Olympia oysters (Ostrea lurida) at the Kenneth K. Chew Center for…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Oyster Sampling - Olympia Oyster OA Populations at Manchester

2016

Miscellaneous

Sep 12, 2016

I helped Katherine Silliman with her oyster sampling today from her ocean acidification experiment with Olympia oysters (Ostrea lurida) at the Kenneth K. Chew Center for…

<<<<<<< HEAD

Sep 12, 2016

We received notice that Jay’s coral (Porites spp) epiRADseq ( dead onsnetwork link jdimond/2016/08/02/rad-sequencing-days-12/) data was available from the Genomic Sequencing…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Received - Jay’s Coral epiRADseq

2016

coral

epiRAD

Porites

RAD

RAD-seq

Sep 8, 2016

We received notice that Jay’s coral (Porites spp) epiRADseq ( dead onsnetwork link jdimond/2016/08/02/rad-sequencing-days-12/) data was available from the Genomic Sequencing…

<<<<<<< HEAD

Sep 8, 2016

Whoops! It’s already September 6th! The 1st of the month came and went without me noticing.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Goals - September 2016

2016

Goals

Sep 6, 2016

Whoops! It’s already September 6th! The 1st of the month came and went without me noticing.

<<<<<<< HEAD

Sep 6, 2016

After a bit of a scare this weekend (Synology DX513 expansion unit no longer detected two drives after a system update - resolved by powering down the system and rebooting…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Management - Synology Cloud Sync to UW Google Drive

2016

Computer Servicing

Aug 29, 2016

After a bit of a scare this weekend (Synology DX513 expansion unit no longer detected two drives after a system update - resolved by powering down the system and rebooting…

<<<<<<< HEAD

Aug 29, 2016

Noticed that Owl (Synology DS1812+ server) was beeping.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Server HDD Failure – Owl

2016

Computer Servicing

Aug 22, 2016

Noticed that Owl (Synology DS1812+ server) was beeping.

<<<<<<< HEAD

Aug 22, 2016

Submitted the following manuscript to PeerJ for peer review:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Manuscript Submission - Oly Stress Response to PeerJ for Review

2016

Miscellaneous

Aug 18, 2016

Submitted the following manuscript to PeerJ for peer review:

<<<<<<< HEAD

Aug 18, 2016

After some basal readings about what Fst is (see notebook below for a definition and reference), I decided to try to use fastStructure to analyze the PyRAD output from 201607…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Analysis - fastStructure Population Analysis of Oly GBS PyRAD Output

2016

Genotype-by-sequencing at BGI

fastStructure

jupyter notebook

olympia oyster

Ostrea lurida

Structure

Aug 16, 2016

After some basal readings about what Fst is (see notebook below for a definition and reference), I decided to try to use fastStructure to analyze the PyRAD output from 201607…

<<<<<<< HEAD

Aug 16, 2016

I recently moved some computing jobs over to Amazon’s Elastic Cloud Computing (EC2) in attempt to avoid some odd computing issues/errors I kept encountering on our lab…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Computing - Amazon EC2 Cost “Analysis”

2016

computing

EC2

Xserve

I recently moved some computing jobs over to Amazon’s Elastic Cloud Computing (EC2) in attempt to avoid some odd computing issues/errors I kept encountering on our lab…

<<<<<<< HEAD

Complete Olympia oyster GBS data analysis - Progress has actually been made! After many struggles, I managed to get a PyRad analysis of the entire data set to complete. Now…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Goals - August 2016

2016

Goals

Complete Olympia oyster GBS data analysis - Progress has actually been made! After many struggles, I managed to get a PyRad analysis of the entire data set to complete. Now…

<<<<<<< HEAD

Previously, I ran a PyRad analysis on just a subset of these samples in an attempt to have some data for a grant pre-proposal.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Analysis - PyRad Analysis of Olympia Oyster GBS Data

2016

Genotype-by-sequencing at BGI

docker

EC2

jupyter notebook

olympia oyster

Ostrea lurida

pyrad

Jul 27, 2016

Previously, I ran a PyRad analysis on just a subset of these samples in an attempt to have some data for a grant pre-proposal.

<<<<<<< HEAD

Jul 27, 2016

Well, I tackled the storage space issue by expanding the EC2 Instance to have a 1000GB of storage space. Now that that’s no longer a concern, it turns out I’m running up…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Computing - Not Enough Power!

2016

computing

EC2

jupyter notebook

pyrad

stacks

ustacks

Jul 18, 2016

Well, I tackled the storage space issue by expanding the EC2 Instance to have a 1000GB of storage space. Now that that’s no longer a concern, it turns out I’m running up…

<<<<<<< HEAD

Jul 18, 2016

Running PyRad analysis on the Olympia oyster GBS data. PyRad exited with warnings about running out of space. However, looking at free disk space on the EC2 Instance…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Computing - Amazon EC2 Instance Out of Space?

2016

Genotype-by-sequencing at BGI

Olympia oyster reciprocal transplant

Jul 17, 2016

Running PyRad analysis on the Olympia oyster GBS data. PyRad exited with warnings about running out of space. However, looking at free disk space on the EC2 Instance…

<<<<<<< HEAD

Jul 17, 2016

Yesterday’s post ended with me trying to mount a S3 bucket to my EC2 instance using s3fs-fuse.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Computing - A Very Quick “Guide” to Amazon EC2 Continued

2016

Miscellaneous

Yesterday’s post ended with me trying to mount a S3 bucket to my EC2 instance using s3fs-fuse.

<<<<<<< HEAD

We’re working on a project with Washington Department of Natural Resources’ (DNR) Micah Horwith to identify potential proteomic biomarkers in geoduck (Panopea generosa) and …

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Dissection - Frozen Geoduck & Pacific Oyster

2016

Miscellaneous

We’re working on a project with Washington Department of Natural Resources’ (DNR) Micah Horwith to identify potential proteomic biomarkers in geoduck (Panopea generosa) and …

<<<<<<< HEAD

Replaced the filters on the rack enclosure that houses the Apple Xserver server blades we have in the lab.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Filter Replacement - Xserve Server Rack Enclosure

2016

Computer Servicing

Replaced the filters on the rack enclosure that houses the Apple Xserver server blades we have in the lab.

<<<<<<< HEAD

This all takes a surprisingly long time to set up.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Computing - The Very Quick “Guide” to Amazon Web Services Cloud Computing Instances (EC2)

2016

Miscellaneous

Jul 13, 2016

This all takes a surprisingly long time to set up.

<<<<<<< HEAD

Jul 13, 2016

Ran the coral DNA I quantified on 20160630 through the MethylFlash Methylated DNA Quantification Kit [Colorimetric] (Epigentek) kit to quantify global methylation.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Methylation Quantification - Coral DNA from Jose M. Eirin-Lopez (Florida International University)

2016

Miscellaneous

Jul 7, 2016

Ran the coral DNA I quantified on 20160630 through the MethylFlash Methylated DNA Quantification Kit [Colorimetric] (Epigentek) kit to quantify global methylation.

<<<<<<< HEAD

Jul 7, 2016

Unfortunately, most of this month’s goals are the same as last months!

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Goals - July 2016

2016

Goals

Jul 1, 2016

Unfortunately, most of this month’s goals are the same as last months!

<<<<<<< HEAD

Jul 1, 2016

Quantified the DNA we received from Jose on 20160615 using the Qubit 3.0 Flouorometer (ThermoFisher) with the dsDNA Broad Range (BR) Kit according to the manufacturer’s…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Quantification - Coral DNA from Jose M. Eirin-Lopez (Florida International University)

2016

Miscellaneous

Jun 30, 2016

Quantified the DNA we received from Jose on 20160615 using the Qubit 3.0 Flouorometer (ThermoFisher) with the dsDNA Broad Range (BR) Kit according to the manufacturer’s…

<<<<<<< HEAD

Jun 30, 2016

Steven received these coral DNA samples today. Here’s his post on Google Plus (stored @ 4C in FTR 213):

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Samples Received - Coral DNA from Jose M. Eirin-Lopez (Florida International University)

2016

Samples Received

Jun 15, 2016

Steven received these coral DNA samples today. Here’s his post on Google Plus (stored @ 4C in FTR 213):

<<<<<<< HEAD

Jun 15, 2016

I noticed a discrepancy between what system info is detected natively on Roadrunner (Apple Xserve) and what was being shown when I started a Docker container.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Docker - VirtualBox Defaults on OS X

2016

Computer Servicing

Jun 14, 2016

I noticed a discrepancy between what system info is detected natively on Roadrunner (Apple Xserve) and what was being shown when I started a Docker container.

<<<<<<< HEAD

Jun 14, 2016

One liner to create Docker container for Jupyter notebook usage and data analysis on roadrunner (Xserve):

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Docker - One liner to create Docker container

2016

Miscellaneous

One liner to create Docker container for Jupyter notebook usage and data analysis on roadrunner (Xserve):

<<<<<<< HEAD

We received the new 48GB RAM set we ordered from Other World Computing for the Apple Xserve (roadrunner) that I installed El Capitan (OS X 10.11.5) on two weeks ago.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RAM Upgrade - Roadrunner (Apple Xserve) to 48GB RAM

2016

Computer Servicing

We received the new 48GB RAM set we ordered from Other World Computing for the Apple Xserve (roadrunner) that I installed El Capitan (OS X 10.11.5) on two weeks ago.

<<<<<<< HEAD

Current goals are as follows:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Goals - June 2016

2016

Goals

Jun 6, 2016

Current goals are as follows:

<<<<<<< HEAD

Jun 6, 2016

In an attempt at furthering our lab’s abilities to maximize our reproducibility, I’ve been working on developing an all-encompassing Docker image. Docker is a type of…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Docker - Improving Roberts Lab Reproducibility

2016

Computer Servicing

Jun 1, 2016

In an attempt at furthering our lab’s abilities to maximize our reproducibility, I’ve been working on developing an all-encompassing Docker image. Docker is a type of…

<<<<<<< HEAD

Jun 1, 2016

Here’s an overview of some of the struggles getting node003 converted/upgraded to function as an independent computer (as opposed to a slave node in the Apple computer…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Computer Setup - Cluster Node003 Conversion

2016

Computer Servicing

May 31, 2016

Here’s an overview of some of the struggles getting node003 converted/upgraded to function as an independent computer (as opposed to a slave node in the Apple computer…

<<<<<<< HEAD

May 31, 2016

This analysis ran (or, more properly, was attempted) for a couple of weeks and failed a few times. The failures seemed to be linked to the external hard drive I was…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Analysis - Oly GBS Data Using Stacks 1.37

2016

Genotype-by-sequencing at BGI

BGI

GBS

genotype-by-sequencing

ipython notebook

jupyter notebook

olympia oyster

Ostrea lurida

stacks

May 23, 2016

This analysis ran (or, more properly, was attempted) for a couple of weeks and failed a few times. The failures seemed to be linked to the external hard drive I was…

<<<<<<< HEAD

May 23, 2016

Received another set of Ostrea lurida genome assembly data from BGI. In this case, it’s data assembled from the small insert libraries they created for this project.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Management - Olympia Oyster Small Insert Library Genome Assembly from BGI

2016

Olympia Oyster Genome Sequencing

BGI

ipython notebook

jupyter notebook

olympia oyster

Ostrea lurida

May 16, 2016

Received another set of Ostrea lurida genome assembly data from BGI. In this case, it’s data assembled from the small insert libraries they created for this project.

<<<<<<< HEAD

May 16, 2016

This isn’t really a notebook entry - it’s more of a traditional blog post.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

GBS Frustrations

2016

Miscellaneous

May 3, 2016

This isn’t really a notebook entry - it’s more of a traditional blog post.

<<<<<<< HEAD

May 3, 2016

Well, I guess the first goal is to remember to be more consistent about writing monthly goals…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Goals - May 2016

2016

Goals

May 2, 2016

Well, I guess the first goal is to remember to be more consistent about writing monthly goals…

<<<<<<< HEAD

May 2, 2016

The RNAseq data that I previously submitted to NCBI short read archive (SRA) has been released to the public today. Here are the various links for the project:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

SRA Release - Transcriptomic Profiles of Adult Female & Male Gonads in Panopea generosa (Pacific geoduck)

2016

Protein expression profiles during sexual maturation in Geoduck

SRA Submissions

geoduck

Panopea generosa

PRJNA316216

SRA

SRP072283

SRX1659865

SRX1659866

Apr 28, 2016

The RNAseq data that I previously submitted to NCBI short read archive (SRA) has been released to the public today. Here are the various links for the project:

<<<<<<< HEAD

Apr 28, 2016

BGI had previously supplied us with demultiplexed GBS FASTQ files. However, they had not provided us with the information/data on how those files were created. I contacted…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Management - O.lurida Raw BGI GBS FASTQ Data

2016

Genotype-by-sequencing at BGI

Olympia oyster reciprocal transplant

BGI had previously supplied us with demultiplexed GBS FASTQ files. However, they had not provided us with the information/data on how those files were created. I contacted…

<<<<<<< HEAD

I decided to run a quick test to see what difference in speed (i.e. time) we might see between handling files that are stored locally, on an external hard drive (HDD), or on…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Computing - Speed Benchmark Comparisons Between Local, External, & Server Files

2016

Miscellaneous

I decided to run a quick test to see what difference in speed (i.e. time) we might see between handling files that are stored locally, on an external hard drive (HDD), or on…

<<<<<<< HEAD

Attempting to get some sort of analysis of the Ostrea lurida GBS data from BGI, particularly since the last run at it using Stacks crashed (literally) and burned (not…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Analysis - Subset Olympia Oyster GBS Data from BGI as Single Population Using PyRAD

2016

Genotype-by-sequencing at BGI

.vcf

IGV

ipython notebook

jupyter notebook

olympia oyster

Ostrea lurida

pyrad

SNPs

Apr 18, 2016

Attempting to get some sort of analysis of the Ostrea lurida GBS data from BGI, particularly since the last run at it using Stacks crashed (literally) and burned (not…

<<<<<<< HEAD

Apr 18, 2016

Steven requested I concatenate the MBDseq files we received for this project:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Management - Concatenate FASTQ files from Oly MBDseq Project

2016

MBD Enrichment for Sequencing at ZymoResearch

Olympia oyster reciprocal transplant

Apr 11, 2016

Steven requested I concatenate the MBDseq files we received for this project:

<<<<<<< HEAD

Apr 11, 2016

UPDATE (20160418) : I’m posting this more for posterity, as Stacks continually locked up at both the “ustacks” and “cstacks” stages. These processes would take days to run…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Analysis - Oly GBS Data from BGI Using Stacks

2016

Genotype-by-sequencing at BGI

UPDATE (20160418) : I’m posting this more for posterity, as Stacks continually locked up at both the “ustacks” and “cstacks” stages. These processes would take days to run…

<<<<<<< HEAD

Getting ready to analyze our Ostrea lurida genotype-by-sequencing data and wanted to use the Stacks software.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Software Install - samtools-0.1.19 and stacks-1.37

2016

Computer Servicing

Getting ready to analyze our Ostrea lurida genotype-by-sequencing data and wanted to use the Stacks software.

<<<<<<< HEAD

Adding our Olympia oyster genome sequencing (sequencing done by BGI) to the NCBI Sequence Read Archive (SRS). The current status can be seen in the screen cap below. Release…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

SRA Submission – Genome sequencing of the Olympia oyster (Ostrea lurida)

2016

Olympia Oyster Genome Sequencing

SRA Submissions

NCBI

olympia oyster

Ostrea lurida

PRJNA316624

SAMN04588827

SRA

SRP072461

SRS1365663

SRX1667397

SRX1667398

SRX1667399

SRX1667400

SRX1667401

SRX1667402

Adding our Olympia oyster genome sequencing (sequencing done by BGI) to the NCBI Sequence Read Archive (SRS). The current status can be seen in the screen cap below. Release…

<<<<<<< HEAD

Adding our geoduck genome sequencing (sequencing done by BGI) to the NCBI Sequence Read Archive (SRS). The current status can be seen in the screen cap below. Release date…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

SRA Submission – Genome sequencing of the Pacific geoduck (Panopea generosa)

2016

Geoduck Genome Sequencing

SRA Submissions

geoduck

NCBI

Panopea generosa

SRA

PRJNA316601

Adding our geoduck genome sequencing (sequencing done by BGI) to the NCBI Sequence Read Archive (SRS). The current status can be seen in the screen cap below. Release date…

<<<<<<< HEAD

RNAseq experiment, which is part of a larger project that involves characterizing geoduck gonad development across multiple stages: histologically, proteomically, and…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

SRA Submission - Transcriptomic Profiles of Adult Female & Male Gonads in Panopea generosa (Pacific geoduck).

2016

Protein expression profiles during sexual maturation in Geoduck

geoduck

NCBI

Panopea generosa

SRA

SRP072283

Mar 24, 2016

RNAseq experiment, which is part of a larger project that involves characterizing geoduck gonad development across multiple stages: histologically, proteomically, and…

<<<<<<< HEAD

Mar 24, 2016

RNA-seq experiment conducted by Claire in 2013.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

SRA Submission - Individual Transcriptomic Profiles of C.gigas Before & After Heat Shock

2016

SRA Submissions

RNA-seq experiment conducted by Claire in 2013.

<<<<<<< HEAD

We have an enormous backlog of high-throughput sequencing files (641 FASTQ files, to be exact) that we need/want to get added to the NCBI Sequence Read Archive (SRA).

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Management - SRA Submission Overview

2016

Miscellaneous

We have an enormous backlog of high-throughput sequencing files (641 FASTQ files, to be exact) that we need/want to get added to the NCBI Sequence Read Archive (SRA).

<<<<<<< HEAD

We received a hard drive from BGI on 20160223 (while I was out on paternity leave) containing the Ostrea lurida GBS data.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Management - O. lurida genotype-by-sequencing (GBS) data from BGI

2016

Genotype-by-sequencing at BGI

We received a hard drive from BGI on 20160223 (while I was out on paternity leave) containing the Ostrea lurida GBS data.

<<<<<<< HEAD

The initial assembly of the Ostrea lurida genome is available from BGI. Currently, we’ve stashed it here:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Received - Initial Geoduck Genome Assembly from BGI

2016

Geoduck Genome Sequencing

The initial assembly of the Ostrea lurida genome is available from BGI. Currently, we’ve stashed it here:

<<<<<<< HEAD

The initial assembly of the Ostrea lurida genome is available from BGI. Currently, we’ve stashed it here:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Received - Initial Olympia oyster Genome Assembly from BGI

2016

Olympia Oyster Genome Sequencing

The initial assembly of the Ostrea lurida genome is available from BGI. Currently, we’ve stashed it here:

<<<<<<< HEAD

An astute observation by Katherine Sillimanrevealed that the FASTQ files I had moved to our high-throughput sequencing archive on our server Owl, only had two FASTQ files…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Management - O.lurida 2bRAD Dec2015 Undetermined FASTQ files

2016

2bRAD Library Tests for Sequencing at Genewiz

Olympia oyster reciprocal transplant

2bRAD

ipython notebook

jupyter notebook

olympia oyster

Ostrea lurida

RAD

RAD-seq

Mar 8, 2016

An astute observation by Katherine Sillimanrevealed that the FASTQ files I had moved to our high-throughput sequencing archive on our server Owl, only had two FASTQ files…

<<<<<<< HEAD

Mar 8, 2016

We’ve had a recent influx of sequencing data, which is great, but it created a bit of a backlog documenting what we’ve received.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Management - High-throughput Sequencing Data

2016

fusion table

nightingales

owl

Feb 4, 2016

We’ve had a recent influx of sequencing data, which is great, but it created a bit of a backlog documenting what we’ve received.

<<<<<<< HEAD

Feb 4, 2016

Received the Olympia oyster, MBD-enriched BS-seq sequencing files (50bp, single read) from ZymoResearch (submitted 20151208). Here’s the sample list:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Received - Ostrea lurida MBD-enriched BS-seq

2016

MBD Enrichment for Sequencing at ZymoResearch

Olympia oyster reciprocal transplant

Feb 3, 2016

Received the Olympia oyster, MBD-enriched BS-seq sequencing files (50bp, single read) from ZymoResearch (submitted 20151208). Here’s the sample list:

<<<<<<< HEAD

Feb 3, 2016

Downloaded data from the BGI project portal to our server, Owl, using the Synology Download Station. Although the BGI portal is aesthetically nice, it’s set up poorly for…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Received - Ostrea lurida genome sequencing files from BGI

2016

Olympia Oyster Genome Sequencing

Downloaded data from the BGI project portal to our server, Owl, using the Synology Download Station. Although the BGI portal is aesthetically nice, it’s set up poorly for…

<<<<<<< HEAD

Downloaded data from the BGI project portal to our server, Owl, using the Synology Download Station. Although the BGI portal is aesthetically nice, it’s set up poorly for…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Received - Panopea generosa genome sequencing files from BGI

2016

Geoduck Genome Sequencing

Downloaded data from the BGI project portal to our server, Owl, using the Synology Download Station. Although the BGI portal is aesthetically nice, it’s set up poorly for…

<<<<<<< HEAD

Recently, we’ve been bumping into our storage limit on Eagle (our Synology DS413):

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Analysis - Identification of duplicate files on Eagle

2016

Computer Servicing

Jan 14, 2016

Recently, we’ve been bumping into our storage limit on Eagle (our Synology DS413):

<<<<<<< HEAD

Jan 14, 2016

Received notice the sequencing data was ready from Genewiz for the samples submitted 20151222.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Received - Bisulfite-treated Illumina Sequencing from Genewiz

2016

BS-seq Libraries for Sequencing at Genewiz

Olympia oyster reciprocal transplant

Jan 8, 2016

Received notice the sequencing data was ready from Genewiz for the samples submitted 20151222.

<<<<<<< HEAD

Jan 8, 2016

The data was made available to use on 20151224 and took two days to download.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Received - Oly 2bRAD Illumina Sequencing from Genewiz

2015

2bRAD Library Tests for Sequencing at Genewiz

Olympia oyster reciprocal transplant

Dec 31, 2015

The data was made available to use on 20151224 and took two days to download.

<<<<<<< HEAD

Dec 31, 2015

Pooled 10ng of each of the libraries prepared yesterday with [TruSeq DNA Methylation Library Kit…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Sample Submission - BS-seq Library Pool to Genewiz

2015

BS-seq Libraries for Sequencing at Genewiz

Olympia oyster reciprocal transplant

Samples Submitted

Pooled 10ng of each of the libraries prepared yesterday with [TruSeq DNA Methylation Library Kit…

<<<<<<< HEAD

Re-quantified the libraries that were completed yesterday using the Qubit3.0 dsDNA HS (high sensitivity) assay because the library concentrations were too low for the normal…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Illumina Methylation Library Quantification - BS-seq Oly/C.gigas Libraries

2015

BS-seq Libraries for Sequencing at Genewiz

Olympia oyster reciprocal transplant

Re-quantified the libraries that were completed yesterday using the Qubit3.0 dsDNA HS (high sensitivity) assay because the library concentrations were too low for the normal…

<<<<<<< HEAD

Took the bisulfite-treated DNA from 20151218 and made Illumina libraries using the [TruSeq DNA Methylation Library Kit…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Illumina Methylation Library Construction - Oly/C.gigas Bisulfite-treated DNA

2015

BS-seq Libraries for Sequencing at Genewiz

Olympia oyster reciprocal transplant

Dec 21, 2015

Took the bisulfite-treated DNA from 20151218 and made Illumina libraries using the [TruSeq DNA Methylation Library Kit…

<<<<<<< HEAD

Dec 21, 2015

Following the guidelines of the [TruSeq DNA Methylation Library Prep Guide…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Bioanalyzer - Bisulfite-treated Oly/C.gigas DNA

2015

BS-seq Libraries for Sequencing at Genewiz

Olympia oyster reciprocal transplant

Following the guidelines of the [TruSeq DNA Methylation Library Prep Guide…

<<<<<<< HEAD

Prepared the RNA Pico 6000 ladder (Agilent) according to the manufacturer’s protocol:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Reagent Prep - RNA Pico 6000 Ladder

2015

Reagent Prep

Prepared the RNA Pico 6000 ladder (Agilent) according to the manufacturer’s protocol:

<<<<<<< HEAD

After confirming that the DNA available for this project looked good, I performed bisulfite treatment on the following gDNA samples:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Bisulfite Treatment - Oly Reciprocal Transplant DNA & C.gigas Lotterhos DNA for BS-seq

2015

BS-seq Libraries for Sequencing at Genewiz

Olympia oyster reciprocal transplant

After confirming that the DNA available for this project looked good, I performed bisulfite treatment on the following gDNA samples:

<<<<<<< HEAD

The gel I ran earlier today looked real rough, due to the fact that I didn’t bother to equalize loading quantities of samples (I just loaded 1μL of all samples regardless of…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Agarose Gel - Oly gDNA for BS-seq Libraries, Take Two

2015

BS-seq Libraries for Sequencing at Genewiz

Olympia oyster reciprocal transplant

The gel I ran earlier today looked real rough, due to the fact that I didn’t bother to equalize loading quantities of samples (I just loaded 1μL of all samples regardless of…

<<<<<<< HEAD

Ran 1μL of each sample from yesterday’s DNA isolation on a 0.8% agarose, low-TAE gel, stained with ethidium bromide.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Agarose Gel - Oly gDNA for BS-seq Libraries

2015

BS-seq Libraries for Sequencing at Genewiz

Olympia oyster reciprocal transplant

Ran 1μL of each sample from yesterday’s DNA isolation on a 0.8% agarose, low-TAE gel, stained with ethidium bromide.

<<<<<<< HEAD

Need DNA to prep our own libraries for bisulfite-treated high-throughput sequencing (BS-seq).

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Isolation - Oly gDNA for BS-seq

2015

BS-seq Libraries for Sequencing at Genewiz

Olympia oyster reciprocal transplant

1NF11

1NF12

1NF13

1NF14

1NF15

1NF16

1NF17

1NF18

2NF1

2NF2

2NF3

2NF4

2NF5

2NF6

2NF7

2NF8

BS-seq

chloroform

DNA Isolation

DNA Quantification

DNazol

Fidalgo Bay

olympia oyster

Ostrea lurida

Oyster Bay

Qubit 3.0

Qubit dsDNA BR

RNAse A

Dec 16, 2015

Need DNA to prep our own libraries for bisulfite-treated high-throughput sequencing (BS-seq).

<<<<<<< HEAD

Dec 16, 2015

Pooled the libraries into a single sample for sequencing on Illumina HiSeq2500 by Genewiz.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Sample Submission - 2bRAD Libraries for Genewiz

2015

2bRAD Library Tests for Sequencing at Genewiz

Olympia oyster reciprocal transplant

Samples Submitted

Pooled the libraries into a single sample for sequencing on Illumina HiSeq2500 by Genewiz.

<<<<<<< HEAD

Received 6 samples from Katie today. The box was labeled and stored @ -20C.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Samples Received - C.gigas Tissue & DNA from Katie Lotterhos

2015

Samples Received

Received 6 samples from Katie today. The box was labeled and stored @ -20C.

<<<<<<< HEAD

We opted to go with ZymoResearch for this project because they could do the bisulfite treatment and finish the sequencing by the end of January.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Sample Submission - Olympia oyster MBD-enriched DNA to ZymoResearch

2015

MBD Enrichment for Sequencing at ZymoResearch

Olympia oyster reciprocal transplant

Samples Submitted

Dec 8, 2015

We opted to go with ZymoResearch for this project because they could do the bisulfite treatment and finish the sequencing by the end of January.

<<<<<<< HEAD

Dec 8, 2015

Yep, BGI still needs more gDNA for the Olympia oyster genome sequencing project. Samples have been quantified via dye-based fluorescence, as opposed to the NanoDrop, so our…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Sample Submission - Additional Olympia Oyster gDNA for Genome Sequencing @ BGI

2015

Olympia Oyster Genome Sequencing

Samples Submitted

Yep, BGI still needs more gDNA for the Olympia oyster genome sequencing project. Samples have been quantified via dye-based fluorescence, as opposed to the NanoDrop, so our…

<<<<<<< HEAD

Yep, BGI still needs more gDNA for the geoduck genome sequencing project. Samples have been quantified via dye-based fluorescence, as opposed to the NanoDrop, so our…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Sample Submission - Additional Geoduck gDNA for Genome Sequencing @ BGI

2015

Geoduck Genome Sequencing

Yep, BGI still needs more gDNA for the geoduck genome sequencing project. Samples have been quantified via dye-based fluorescence, as opposed to the NanoDrop, so our…

<<<<<<< HEAD

Running a bit low on storage on Owl (Synology DS1812+) and we will be receiving a ton of data in the next few months, so we purchased a Synology DX513. It’s an expansion…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Storage - Synology DX513

2015

Computer Servicing

Running a bit low on storage on Owl (Synology DS1812+) and we will be receiving a ton of data in the next few months, so we purchased a Synology DX513. It’s an expansion…

<<<<<<< HEAD

Sent Olympia oyster tissue samples to BGI for genotype-by-sequencing (GBS). Tissues were shipped FedEx standard overnight on dry ice.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Sample Submission - Oly Oyster Bay Tissues for GBS

2015

Genotype-by-sequencing at BGI

Olympia oyster reciprocal transplant

Samples Submitted

Sent Olympia oyster tissue samples to BGI for genotype-by-sequencing (GBS). Tissues were shipped FedEx standard overnight on dry ice.

<<<<<<< HEAD

Samples were stored @ -20C in FTR 209.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Samples Received - Oly Tissue & DNA from Katherine Silliman

2015

Olympia oyster reciprocal transplant

Samples Received

Samples were stored @ -20C in FTR 209.

<<<<<<< HEAD

Have three separate sets of geoduck & olympia oyster gDNA that need to be run on gels before sending to BGI for genome sequencing:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Quality Assessment - Geoduck & Olympia Oyster gDNA

2015

Geoduck Genome Sequencing

Olympia Oyster Genome Sequencing

gDNA

gel

geoduck

O'geneRuler DNA Ladder Mix

olympia oyster

Ostrea lurida

Panopea generosa

`Nov 25, 2015`{=html}

Isolated additional gDNA for the genome sequencing. To try to improve the quality (260/280 & 260/230 ratios) of the gDNA, I added a chloroform step after the initial tissue…

<<<<<<< HEAD

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Isolation - Olympia Oyster Outer Mantle gDNA

2015

Olympia Oyster Genome Sequencing

chloroform

DNA Isolation

DNA Quantification

DNazol

gDNA

mantle

NanoDrop1000

olympia oyster

Ostrea lurida

Qubit 3.0

Qubit dsDNA BR

Isolated additional gDNA for the genome sequencing. To try to improve the quality (260/280 & 260/230 ratios) of the gDNA, I added a chloroform step after the initial tissue…

<<<<<<< HEAD

Isolated additional gDNA for the genome sequencing. In an attempt to obtain better yields, I used ctenidia (instead of adductor muscle). Additionally, to try to improve the…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Isolation - Geoduck Ctenidia gDNA

2015

Geoduck Genome Sequencing

chloroform

ctenidia

DNA Isolation

DNA Quantification

DNazol

gDNA

geoduck

NanoDrop1000

Panopea generosa

Qubit 3.0

Qubit dsDNA BR

Isolated additional gDNA for the genome sequencing. In an attempt to obtain better yields, I used ctenidia (instead of adductor muscle). Additionally, to try to improve the…

<<<<<<< HEAD

The gDNA I extracted on 20151104 didn’t look great on the NanoDrop so I decided to perform a phenol-chloroform cleanup to see if I could improve the NanoDrop1000 absorbance…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Phenol-Chloroform DNA Cleanup - Geoduck gDNA

2015

Geoduck Genome Sequencing

DNA Quantification

gDNA

geoduck

NanoDrop1000

Panopea generosa

phenol-chloroform cleanup

Quant-iT DNA BR Kit

Victor 1420 plate reader

The gDNA I extracted on 20151104 didn’t look great on the NanoDrop so I decided to perform a phenol-chloroform cleanup to see if I could improve the NanoDrop1000 absorbance…

<<<<<<< HEAD

The gDNA I extracted on 20151104 didn’t look great on the NanoDrop so I decided to perform a phenol-chloroform cleanup to see if I could improve the NanoDrop1000 absorbance…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Phenol-Chloroform DNA Cleanup - Olympia Oyster gDNA

2015

Olympia Oyster Genome Sequencing

The gDNA I extracted on 20151104 didn’t look great on the NanoDrop so I decided to perform a phenol-chloroform cleanup to see if I could improve the NanoDrop1000 absorbance…

<<<<<<< HEAD

Since we still don’t have sufficient gDNA for the full scope of the genome sequencing, I isolated more gDNA.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Isolation - Geoduck Adductor Muscle gDNA

2015

Geoduck Genome Sequencing

DNA Isolation

DNA Quantification

gDNA

geoduck

NanoDrop1000

Panopea generosa

Quant-iT DNA BR Kit

Victor 1420 plate reader

Since we still don’t have sufficient gDNA for the full scope of the genome sequencing, I isolated more gDNA.

<<<<<<< HEAD

Since we still don’t have sufficient gDNA for the full scope of the Olympia oyster genome sequencing, I isolated more gDNA.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Isolation - Olympia Oyster Outer Mantle gDNA

2015

Olympia Oyster Genome Sequencing

DNA Isolation

DNA Quantification

E.Z.N.A. Mollusc Kit

gDNA

NanoDrop1000

olympia oyster

Ostrea lurida

Quant-iT DNA BR Kit

Victor 1420 plate reader

Since we still don’t have sufficient gDNA for the full scope of the Olympia oyster genome sequencing, I isolated more gDNA.

<<<<<<< HEAD

Quantified the MBD enriched samples prepped over the last two days: MBD enrichment, EtOH precipiation.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Quantification - MBD-enriched Olympia oyster DNA

2015

MBD Enrichment for Sequencing at ZymoResearch

Olympia oyster reciprocal transplant

DNA Quantification

MBD

MBD-Seq

olympia oyster

Ostrea lurida

plate reader

Quant-iT DNA BR Kit

Victor 1420 plate reader

Nov 23, 2015

Quantified the MBD enriched samples prepped over the last two days: MBD enrichment, EtOH precipiation.

<<<<<<< HEAD

Nov 23, 2015

Precipitated the MBD enriched DNA from yesterday according to the MethylMiner Methylated DNA Enrichment Kit (Invitrogen) protocol.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Ethanol Precipitation - Olympia oyster MBD

2015

MBD Enrichment for Sequencing at ZymoResearch

Olympia oyster reciprocal transplant

EtOH precipitation

MethylMiner Methylated DNA Enrichment Kit

olympia oyster

Ostrea lurida

Nov 22, 2015

Precipitated the MBD enriched DNA from yesterday according to the MethylMiner Methylated DNA Enrichment Kit (Invitrogen) protocol.

<<<<<<< HEAD

Nov 22, 2015

Olympia oyster gDNA that had previously been sonicated and fragmented was enriched for the methylated fragments using the MethylMiner Methylated DNA Enrichment Kit…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

MBD Enrichment - Sonicated Olympia Oyster gDNA

2015

MBD Enrichment for Sequencing at ZymoResearch

Olympia oyster reciprocal transplant

hc1_2B

hc1_4B

hc2_15B

hc2_17

hc3_1

hc3_10

hc3_11

hc3_5

hc3_7

hc3_9

Hood Canal

MethylMiner Methylated DNA Enrichment Kit

olympia oyster

Ostrea lurida

Oyster Bay

ss2_14B

ss2_18B

ss2_9B

ss3_14B

ss3_15B

ss3_16B

ss3_20

ss3_3B

ss3_4B

ss5_18

Nov 21, 2015

Olympia oyster gDNA that had previously been sonicated and fragmented was enriched for the methylated fragments using the MethylMiner Methylated DNA Enrichment Kit…

<<<<<<< HEAD

Nov 21, 2015

In preparation for MBD enrichment, fragmented Olympia oyster gDNA with a target size of ~350bp.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Sonication - Oly gDNA for MBD

2015

MBD Enrichment for Sequencing at ZymoResearch

bioanalyzer

Bioruptor 300

electropherogram

hc1_2B

hc1_4B

hc2_15B

hc2_17

hc3_1

hc3_10

hc3_11

hc3_5

hc3_7

hc3_9

Hood Canal

olympia oyster

Ostrea lurida

Oyster Bay

sonication

ss2_14B

ss2_18B

ss2_9B

ss3_14B

ss3_15B

ss3_16B

ss3_20

ss3_3B

ss3_4B

ss5_18

Nov 19, 2015

In preparation for MBD enrichment, fragmented Olympia oyster gDNA with a target size of ~350bp.

<<<<<<< HEAD

Nov 19, 2015

After yesterday’s attempt at quantification revealed insufficient dilution of the libraries, I repeated the qPCRs using 1:100000 dilutions of each of the libraries. Used the…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR – Oly RAD-Seq Library Quantification

2015

2bRAD Library Tests for Sequencing at Genewiz

Olympia oyster reciprocal transplant

2bRAD

KAPA Library Illumina Quantification Kit

olympia oyster

Opticon

Opticon2

Ostrea lurida

qPCR

RAD

RAD-seq

Nov 17, 2015

After yesterday’s attempt at quantification revealed insufficient dilution of the libraries, I repeated the qPCRs using 1:100000 dilutions of each of the libraries. Used the…

<<<<<<< HEAD

Nov 17, 2015

The final step before sequencing these 2bRAD libraries is to quantify them. Used the KAPA Illumina Quantification Kit (KAPA Biosystems) according to the manufacturer’s…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Oly RAD-Seq Library Quantification

2015

2bRAD Library Tests for Sequencing at Genewiz

Olympia oyster reciprocal transplant

2bRAD

KAPA Library Illumina Quantification Kit

olympia oyster

Opticon

Opticon2

Ostrea lurida

qPCR

RAD

RAD-seq

The final step before sequencing these 2bRAD libraries is to quantify them. Used the KAPA Illumina Quantification Kit (KAPA Biosystems) according to the manufacturer’s…

<<<<<<< HEAD

Extracted the PCR products from the gel slices from 20151114 using the QIAQuick Gel Extraction Kit (Qiagen) according to the manufacturer’s protocol. Substituted MiniElute…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Gel Extraction - Oly RAD-Seq Prep Scale PCR

2015

2bRAD Library Tests for Sequencing at Genewiz

Olympia oyster reciprocal transplant

2bRAD

gel extraction

olympia oyster

Ostrea lurida

QIAQuick Gel Extraction Kit

RAD

RAD-seq

Extracted the PCR products from the gel slices from 20151114 using the QIAQuick Gel Extraction Kit (Qiagen) according to the manufacturer’s protocol. Substituted MiniElute…

<<<<<<< HEAD

I recently ran gDNA isolated for geoduck and Olympia oyster genome sequencing, as well as gDNA isolated from the Olympia oyster reciprocal transplant experiment out on a…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Quality Assessment - Geoduck, Oly & Oly 2SN

2015

Geoduck Genome Sequencing

Olympia Oyster Genome Sequencing

Olympia oyster reciprocal transplant

Fidalgo 2SN

gDNA

gel

geoduck

O'geneRuler DNA Ladder Mix

olympia oyster

Ostrea lurida

Panopea generosa

`Nov 13, 2015`{=html}

Continuing with the RAD-seq library prep. Following the Meyer Lab 2bRAD protocol. After determining the minimum number of PCR cycles to run to generate a visible, 166bp band…

<<<<<<< HEAD

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

PCR – Oly RAD-seq Prep Scale PCR

2015

2bRAD Library Tests for Sequencing at Genewiz

Olympia oyster reciprocal transplant

barcodes

gel

ILL-BC1

ILL-BC10

ILL-BC2

ILL-BC3

ILL-BC4

ILL-BC5

ILL-BC6

ILL-BC7

ILL-BC8

ILL-BC9

ILL-HT1

olympia oyster

Ostrea lurida

PCR

PTC-200

Q5 High-Fidelity DNA Polymerase

RAD

RAD-seq

Nov 13, 2015

Continuing with the RAD-seq library prep. Following the Meyer Lab 2bRAD protocol. After determining the minimum number of PCR cycles to run to generate a visible, 166bp band…

<<<<<<< HEAD

Nov 13, 2015

Continuing with the RAD-seq library prep. Following the Meyer Lab 2bRAD protocol.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

PCR – Oly RAD-seq Test-scale PCR

2015

2bRAD Library Tests for Sequencing at Genewiz

Olympia oyster reciprocal transplant

gel

ILL-BC1

ILL-HT1

ILL-LIB1

ILL-LIB2

O'geneRuler DNA Ladder Mix

olympia oyster

Ostrea lurida

PCR

PTC-200

RAD

RAD-seq

`Nov 12, 2015`{=html}

Comparison of three different approaches to using the E.Z.N.A. Mollusc Kit:

<<<<<<< HEAD

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Quantification & Quality Assessment - Oly 2SN gDNA

2015

Olympia oyster reciprocal transplant

bioanalyzer

DNA Quantification

Fidalgo 2SN

gDNA

NanoDrop1000

olympia oyster

Ostrea lurida

Comparison of three different approaches to using the E.Z.N.A. Mollusc Kit:

<<<<<<< HEAD

Quantified the following samples with the Roberts Lab NanoDrop1000 (ThermoFisher) and assessed DNA integrity on the Seeb Lab Bioanalyzer 2100 (Agilent) using the DNA 12000…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Quantification & Quality Assessment - Geoduck & Oly gDNA

2015

Geoduck Genome Sequencing

Olympia Oyster Genome Sequencing

bioanalyzer

DNA Quantification

gDNA

geoduck

NanoDrop1000

olympia oyster

Ostrea lurida

Panopea generosa

Quantified the following samples with the Roberts Lab NanoDrop1000 (ThermoFisher) and assessed DNA integrity on the Seeb Lab Bioanalyzer 2100 (Agilent) using the DNA 12000…

<<<<<<< HEAD

Isolated DNA from 24 2SN ctenidia samples from Friday’s sampling (#32 - 55). Samples were thawed at RT.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Isolations – Oly Fidalgo 2SN Ctenidia

2015

Olympia oyster reciprocal transplant

DNA Isolation

E.Z.N.A. Mollusc Kit

Fidalgo 2SN

gDNA

olympia oyster

Ostrea lurida

Nov 3, 2015

Isolated DNA from 24 2SN ctenidia samples from Friday’s sampling (#32 - 55). Samples were thawed at RT.

<<<<<<< HEAD

Nov 3, 2015

The remaining Olympia oysters from Jake Heare’s reciprocal transplant experiment have been retrieved from field sites and are awaiting sampling. The oysters have been stored…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Oyster Sampling - Oly Fidalgo 2SN, 2HL, 2NF Reciprocal Transplants Final Samplings

2015

Olympia oyster reciprocal transplant

ctenidia

E.Z.N.A. Mollusc Kit

Fidalgo 2HL

Fidalgo 2NF

Fidalgo 2SN

gill

olympia oyster

Ostrea lurida

RNAlater

Oct 30, 2015

The remaining Olympia oysters from Jake Heare’s reciprocal transplant experiment have been retrieved from field sites and are awaiting sampling. The oysters have been stored…

<<<<<<< HEAD

Oct 30, 2015

Amazingly, we need more gDNA for the two genome sequencing projects (geoduck and Olympia oyster). Used geoduck adductor muscle sample from Box 1 of the geoduck samples…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Isolation – Geoduck & Olympia Oyster

2015

Geoduck Genome Sequencing

Olympia Oyster Genome Sequencing

DNA Isolation

DNA Quantification

gDNA

geoduck

NanoDrop1000

olympia oyster

Ostrea lurida

Panopea generosa

Amazingly, we need more gDNA for the two genome sequencing projects (geoduck and Olympia oyster). Used geoduck adductor muscle sample from Box 1 of the geoduck samples…

<<<<<<< HEAD

Continued to follow the 2bRAD protocol (PDF) developed by Eli Meyer’s lab.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Adaptor Ligation – Oly AlfI-Digested gDNA for RAD-seq

2015

2bRAD Library Tests for Sequencing at Genewiz

Olympia oyster reciprocal transplant

3ILL-NR

5ILL-NR

anti-ILL

gDNA

ligation

olympia oyster

Ostrea lurida

PTC-200

RAD-seq

T4 DNA Ligase

Continued to follow the 2bRAD protocol (PDF) developed by Eli Meyer’s lab.

<<<<<<< HEAD

The previous attempt at making these RAD libraries failed during the prep-scale PCR, likely due to a discrepancy in the version of the Meyer Lab protocol I was following, so…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Restriction Digest – Oly gDNA for RAD-seq w/AlfI

2015

2bRAD Library Tests for Sequencing at Genewiz

Olympia oyster reciprocal transplant

2bRAD

AlfI

gDNA

olympia oyster

Ostrea lurida

RAD-seq

restriction digestion

Oct 28, 2015

The previous attempt at making these RAD libraries failed during the prep-scale PCR, likely due to a discrepancy in the version of the Meyer Lab protocol I was following, so…

<<<<<<< HEAD

Oct 28, 2015

Oddly, it turns out that Katherine’s version of the Meyer Lab 2bRAD protocol differed from what I had download. To add to the confusion, both protocols have the same file…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Troubleshooting - Oly RAD-seq

2015

2bRAD Library Tests for Sequencing at Genewiz

Olympia oyster reciprocal transplant

RAD

RAD-seq

troubleshooting

Oct 23, 2015

Oddly, it turns out that Katherine’s version of the Meyer Lab 2bRAD protocol differed from what I had download. To add to the confusion, both protocols have the same file…

<<<<<<< HEAD

Oct 23, 2015

The remaining Olympia oysters from Jake Heare’s reciprocal transplant experiment have been retrieved from field sites and are awaiting sampling. The oysters have been stored…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Isolations - Fidalgo 2SN Reciprocal Transplants Final Samplings

2015

Olympia oyster reciprocal transplant

ctenidia

DNA Isolation

E.Z.N.A. Mollusc Kit

Fidalgo 2SN

olympia oyster

Ostrea lurida

RNAlater

Oct 21, 2015

The remaining Olympia oysters from Jake Heare’s reciprocal transplant experiment have been retrieved from field sites and are awaiting sampling. The oysters have been stored…

<<<<<<< HEAD

Oct 21, 2015

Continuing with the RAD-seq library prep. Following the Meyer Lab 2bRAD protocol.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

PCR - Oly RAD-seq Prep Scale PCR

2015

2bRAD Library Tests for Sequencing at Genewiz

Olympia oyster reciprocal transplant

gel

ILL-BC1

ILL-BC10

ILL-BC2

ILL-BC3

ILL-BC4

ILL-BC5

ILL-BC6

ILL-BC7

ILL-BC8

ILL-BC9

ILL-HT1

ILL-LIB1

ILL-LIB2

olympia oyster

Ostrea lurida

PCR

PTC-200

Q5 High-Fidelity DNA Polymerase

RAD-seq

Oct 13, 2015

Continuing with the RAD-seq library prep. Following the Meyer Lab 2bRAD protocol.

<<<<<<< HEAD

Oct 13, 2015

Continuing with the RAD-seq library prep. Following the Meyer Lab 2bRAD protocol.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

PCR - Oly RAD-seq Test-scale PCR

2015

2bRAD Library Tests for Sequencing at Genewiz

Olympia oyster reciprocal transplant

gel

ILL-BC1

ILL-HT1

ILL-LIB1

ILL-LIB2

O'geneRuler DNA Ladder Mix

olympia oyster

Ostrea lurida

PCR

PTC-200

RAD

RAD-seq

`Oct 12, 2015`{=html}

Continued to follow the 2bRAD protocol (PDF) developed by Eli Meyer’s lab.

<<<<<<< HEAD

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Adaptor Ligation – Oly AlfI-Digested gDNA for RAD-seq

2015

2bRAD Library Tests for Sequencing at Genewiz

Olympia oyster reciprocal transplant

3ILL-NR

5ILL-NR

anti-ILL

ligation

olympia oyster

Ostrea lurida

PTC-200

RAD-seq

T4 DNA Ligase

Continued to follow the 2bRAD protocol (PDF) developed by Eli Meyer’s lab.

<<<<<<< HEAD

Used a subset (10 samples) from the Ostrea lurida gDNA isolated 20150917 to prepare RAD libraries.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Restriction Digest – Oly gDNA for RAD-seq w/AlfI

2015

2bRAD Library Tests for Sequencing at Genewiz

Olympia oyster reciprocal transplant

Used a subset (10 samples) from the Ostrea lurida gDNA isolated 20150917 to prepare RAD libraries.

<<<<<<< HEAD

Previous shipment of gDNA proved to be of insufficient quantity when assessed by BGI, so needed to isolate more.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Sample Submission - Additional Geoduck gDNA for Genome Sequencing @ BGI

2015

Geoduck Genome Sequencing

'1510071003'

gDNA

geoduck

Panopea generosa

Samples Submitted

`Oct 6, 2015`{=html}

Previous shipment of gDNA proved to be of insufficient quantity when assessed by BGI, so needed to isolate more.

<<<<<<< HEAD

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Sample Submission - Additional Olympia Oyster gDNA for Genome Sequencing @ BGI

2015

Olympia Oyster Genome Sequencing

Samples Submitted

'1510071002'

gDNA

olympia oyster

Ostrea lurida

`Oct 6, 2015`{=html}

Needed to assess the integrity of the newest gDNA isolated for the two genome sequencing projects: Geoduck gDNA from earlier today and Olympia oyster gDNA from 20151003.

<<<<<<< HEAD

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Agarose Gel - Geoduck & Olympia Oyster gDNA

2015

Geoduck Genome Sequencing

Olympia Oyster Genome Sequencing

Olympia oyster reciprocal transplant

gDNA

gel

geoduck

NF1A

olympia oyster

Ostrea lurida

Panopea generosa

SN49A

Needed to assess the integrity of the newest gDNA isolated for the two genome sequencing projects: Geoduck gDNA from earlier today and Olympia oyster gDNA from 20151003.

<<<<<<< HEAD

Pooled the gDNA samples from earlier today & from 20151003.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Quantification - Pooled geoduck gDNA

2015

Geoduck Genome Sequencing

DNA Quantification

gDNA

geoduck

NanoDrop1000

Panopea generosa

Pooled the gDNA samples from earlier today & from 20151003.

<<<<<<< HEAD

My isolation on Friday didn’t yield a sufficient quantity of gDNA for the additional DNA needed for the geoduck genome sequencing project. Used two adductor muscles (Box 1)…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

gDNA Isolation - Geoduck Adductor Muscle

2015

adductor muscle

DNA Isolation

DNA Quantification

DNazol

gDNA

geoduck

NanoDrop1000

Panopea generosa

My isolation on Friday didn’t yield a sufficient quantity of gDNA for the additional DNA needed for the geoduck genome sequencing project. Used two adductor muscles (Box 1)…

<<<<<<< HEAD

Amazingly, we need more gDNA for the two genome sequencing projects (geoduck and Olympia oyster). Used geoduck “foot 1” sample from Box 1 of the foot samples collected by…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Isolation - Geoduck & Olympia Oyster

2015

Geoduck Genome Sequencing

Olympia Oyster Genome Sequencing

Olympia oyster reciprocal transplant

adductor muscle

DNA Isolation

DNA Quantification

DNazol

foot

geoduck

NanoDrop1000

NF1A

olympia oyster

Ostrea lurida

Panopea generosa

RNAse A

SN49A

Oct 2, 2015

Amazingly, we need more gDNA for the two genome sequencing projects (geoduck and Olympia oyster). Used geoduck “foot 1” sample from Box 1 of the foot samples collected by…

<<<<<<< HEAD

Oct 2, 2015

Yesterday’s test scale PCR failed to produce any bands in any samples (expected size of ~166bp). This is not particularly surprising, due to the level of degradation in…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

PCR - Oly RAD-seq Test-scale PCR

2015

2bRAD Library Tests for Sequencing at Genewiz

Olympia oyster reciprocal transplant

gel

ILL-BC1

ILL-HT1

ILL-LIB1

ILL-LIB2

O'geneRuler DNA Ladder Mix

olympia oyster

Ostrea lurida

PCR

PTC-200

Q5 High-Fidelity DNA Polymerase

RAD-seq

`Oct 2, 2015`{=html}

Continuing with the RAD-seq library prep. Following the Meyer Lab 2bRAD protocol.

<<<<<<< HEAD

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

PCR - Oly RAD-seq Test-scale PCR

2015

2bRAD Library Tests for Sequencing at Genewiz

Olympia oyster reciprocal transplant

Reagent Prep

gel

ILL-BC1

ILL-HT1

ILL-HT2

ILL-LIB1

ILL-LIB2

O'geneRuler DNA Ladder Mix

olympia oyster

Ostrea lurida

PCR

PTC-200

Q5 High-Fidelity DNA Polymerase

RAD-seq

`Oct 1, 2015`{=html}

Yesterday’s AlfI over night restriction digest was heat inactivated by heating @ 65C for 10mins. Samples were stored on ice.

<<<<<<< HEAD

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Adaptor Ligation - Oly AlfI-Digested gDNA for RAD-seq

2015

2bRAD Library Tests for Sequencing at Genewiz

Olympia oyster reciprocal transplant

Reagent Prep

3ILL-NR

5ILL-NR

anti-ILL

ILL-BC1

ILL-HT1

ILL-HT2

ILL-LIB1

ILL-LIB2

ligation

olympia oyster

Ostrea lurida

PTC-200

RAD-seq

T4 DNA Ligase

Yesterday’s AlfI over night restriction digest was heat inactivated by heating @ 65C for 10mins. Samples were stored on ice.

<<<<<<< HEAD

I’d review last month’s goals, but I completely forgot to post them!

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Goals - October 2015

2015

Goals

geoduck

olympia oyster

Ostrea lurida

Panopea generosa

I’d review last month’s goals, but I completely forgot to post them!

<<<<<<< HEAD

Used a subset (10 samples) from the Ostrea lurida gDNA isolated 20150916 to prepare RAD libraries. This will be done to assess whether or not these samples, which appear to…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Restriction Digest - Oly gDNA for RAD-seq w/AlfI

2015

2bRAD Library Tests for Sequencing at Genewiz

Olympia oyster reciprocal transplant

Reagent Prep

AlfI

gDNA

olympia oyster

Ostrea lurida

RAD-seq

restriction digestion

Sep 30, 2015

Used a subset (10 samples) from the Ostrea lurida gDNA isolated 20150916 to prepare RAD libraries. This will be done to assess whether or not these samples, which appear to…

<<<<<<< HEAD

Sep 30, 2015

Shipped the pooled gDNA we’ve been accumulating to BGI to initiate the Olympia oyster genome sequencing project.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Sample Submission - Olympia Oyster gDNA for Genome Sequencing @ BGI

2015

Olympia Oyster Genome Sequencing

Samples Submitted

1509191001

gDNA

olympia oyster

Ostrea lurida

Shipped the pooled gDNA we’ve been accumulating to BGI to initiate the Olympia oyster genome sequencing project.

<<<<<<< HEAD

Shipped the pooled gDNA we’ve been accumulating to BGI to initiate the geoduck genome sequencing project.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Sample Submission - Geoduck gDNA for Genome Sequencing @ BGI

2015

Geoduck Genome Sequencing

1509191002

gDNA

geoduck

Panopea generosa

Samples Submitted

Shipped the pooled gDNA we’ve been accumulating to BGI to initiate the geoduck genome sequencing project.

<<<<<<< HEAD

A new UPS we installed this week for our qPCR machine (Opticon2 - BioRad) to handle power surges and power outages doesn’t seem to be working properly. With the qPCR machine…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Uninterruptible Power Supplies (UPS)

2015

Computer Servicing

Eagle

Opticon

owl

Synology

uninterruptible power supply

UPS

Sep 18, 2015

A new UPS we installed this week for our qPCR machine (Opticon2 - BioRad) to handle power surges and power outages doesn’t seem to be working properly. With the qPCR machine…

<<<<<<< HEAD

Sep 18, 2015

Ran a 0.8% agarose, 1x modified TAE gel (w/EtBr) with geoduck and Olympia oyster gDNA that was precipitated earlier today. Used 5μL of each sample (~500ng).

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Agarose Gel - Geoduck & Olympia oyster gDNA Integrity Check

2015

Geoduck Genome Sequencing

Olympia Oyster Genome Sequencing

gDNA

gel

geoduck

O'geneRuler DNA Ladder Mix

olympia oyster

Ostrea lurida

Panopea generosa

`Sep 17, 2015`{=html}

Pooled all of the geoduck gDNA from all the previous geoduck isolations for the Geoduck Genome Sequencing Project and pooled all of the Ostrea lurida gDNA from previous…

<<<<<<< HEAD

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Ethanol Precipitation - Geoduck & Olympia oyster gDNA

2015

Geoduck Genome Sequencing

Olympia Oyster Genome Sequencing

DNA Quantification

EtOH precipitation

geoduck

NanoDrop1000

olympia oyster

Ostrea lurida

Panopea generosa

Sep 17, 2015

Pooled all of the geoduck gDNA from all the previous geoduck isolations for the Geoduck Genome Sequencing Project and pooled all of the Ostrea lurida gDNA from previous…

<<<<<<< HEAD

Sep 17, 2015

Ran the gDNA isolated yesterday from Ostrea lurida whole body on a 0.8% modified TAE gel (w/EtBr) to assess gDNA integrity. Used 1μL of each sample.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Agarose Gel - Olympia oyster Whole Body gDNA Integrity Check

2015

2bRAD Library Tests for Sequencing at Genewiz

Olympia oyster reciprocal transplant

gDNA

gel

O'geneRuler DNA Ladder Mix

olympia oyster

Ostrea lurida

`Sep 17, 2015`{=html}

Continued the extractions that Steven began yesterday (dead link - onsnetwork.org/halfshell/2015/09/15/upon-improving-extractions/) and this morning (dead link -…

<<<<<<< HEAD

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Isolation - Olympia oyster whole body

2015

2bRAD Library Tests for Sequencing at Genewiz

Olympia oyster reciprocal transplant

DNA Isolation

DNA Quantification

E.Z.N.A. Mollusc Kit

gDNA

NanoDrop1000

olympia oyster

Ostrea lurida

Continued the extractions that Steven began yesterday (dead link - onsnetwork.org/halfshell/2015/09/15/upon-improving-extractions/) and this morning (dead link -…

<<<<<<< HEAD

Ran 0.8% agarose 1x modified TAE gel stained with EtBr to assess the integrity of geoduck gDNA isolated earlier today.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Agarose Gel – Geoduck gDNA Integrity Check

2015

Geoduck Genome Sequencing

gDNA

gel

geoduck

O'geneRuler DNA Ladder Mix

Panopea generosa

`Sep 16, 2015`{=html}

Just need a tad bit more gDNA for the geoduck genome sequencing project with BGI. Currently have ~69 and need a minimum of 73μg.

<<<<<<< HEAD

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genomic DNA Isolation – Geoduck Adductor Muscle & Foot

2015

Geoduck Genome Sequencing

DNA Isolation

DNA Quantification

DNazol

gDNA

geoduck

NanoDrop1000

Panopea generosa

Just need a tad bit more gDNA for the geoduck genome sequencing project with BGI. Currently have ~69 and need a minimum of 73μg.

<<<<<<< HEAD

Ran 0.8% agarose 1x modified TAE gel stained with EtBr to assess the integrity of geoduck gDNA and Olympia oyster gDNA isolated earlier today.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Agarose Gel - Geoduck & Olympia Oyster gDNA Integrity Check

2015

Geoduck Genome Sequencing

Olympia Oyster Genome Sequencing

gDNA

gel

geoduck

O'geneRuler DNA Ladder Mix

olympia oyster

Ostrea lurida

Panopea generosa

`Sep 15, 2015`{=html}

Isolated gDNA from Ostrea lurida (Olympia oyster) adductor muscle & mantle samples collected by Brent & Steven on 20150812 using DNAzol (Molecular Research Center) according…

<<<<<<< HEAD

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genomic DNA Isolation – Olympia oyster adductor musle & mantle

2015

Olympia Oyster Genome Sequencing

DNA Isolation

DNA Quantification

DNazol

gDNA

NanoDrop1000

olympia oyster

Ostrea lurida

Isolated gDNA from Ostrea lurida (Olympia oyster) adductor muscle & mantle samples collected by Brent & Steven on 20150812 using DNAzol (Molecular Research Center) according…

<<<<<<< HEAD

Isolated gDNA from Panopea generosa (geoduck) adductor muscle & foot samples collected by Brent & Steven on 20150811 using the DNAzol (Molecular Research Center) according…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genomic DNA Isolation – Geoduck Adductor Muscle & Foot

2015

Geoduck Genome Sequencing

DNA Isolation

DNA Quantification

DNazol

gDNA

geoduck

NanoDrop1000

Panopea generosa

Isolated gDNA from Panopea generosa (geoduck) adductor muscle & foot samples collected by Brent & Steven on 20150811 using the DNAzol (Molecular Research Center) according…

<<<<<<< HEAD

Ran 0.8% agarose 1x modified TAE gel stained with EtBr to assess the integrity of geoduck gDNA and Olympia oyster gDNA isolated yesterday.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Agarose Gel - Geoduck & Olympia Oyster gDNA Integrity Check

2015

Geoduck Genome Sequencing

Olympia Oyster Genome Sequencing

gDNA

gel

geoduck

O'geneRuler DNA Ladder Mix

olympia oyster

Ostrea lurida

Panopea generosa

`Sep 15, 2015`{=html}

Previously isolated gDNA from these tissues on 20150902. However, found out after the isolations that BGI needs >73μg of gDNA for the genome sequencing project, which is…

<<<<<<< HEAD

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genomic DNA Isolation - Olympia oyster adductor musle & mantle

2015

Olympia Oyster Genome Sequencing

adductor muscle

DNA Isolation

DNA Quantification

gDNA

mantle

NanoDrop1000

olympia oyster

Ostrea lurida

Previously isolated gDNA from these tissues on 20150902. However, found out after the isolations that BGI needs >73μg of gDNA for the genome sequencing project, which is…

<<<<<<< HEAD

Previously isolated gDNA from these tissues on 20150829. However, found out after the isolations that BGI needs >73μg of gDNA for the genome sequencing project, which is…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genomic DNA Isolation - Geoduck Adductor Muscle & Foot

2015

Geoduck Genome Sequencing

adductor muscle

DNA Isolation

DNA Quantification

DNazol

foot

gDNA

geoduck

NanoDrop1000

Panopea generosa

Previously isolated gDNA from these tissues on 20150829. However, found out after the isolations that BGI needs >73μg of gDNA for the genome sequencing project, which is…

<<<<<<< HEAD

Ran 0.8% agarose 1x modified TAE gel stained with EtBr to assess the integrity of geoduck gDNA (from 20150829) and Olympia oyster gDNA (from 20150902).

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Agarose Gel - Geoduck & Olympia Oyster gDNA Integrity Check

2015

Geoduck Genome Sequencing

Olympia Oyster Genome Sequencing

gDNA

gel

geoduck

O'geneRuler DNA Ladder Mix

olympia oyster

Ostrea lurida

Panopea generosa

`Sep 1, 2015`{=html}

Isolated gDNA from Ostrea lurida (Olympia oyster) adductor muscle & mantle samples collected by Brent & Steven on 20150812 using the E.Z.N.A Mollusc DNA Kit (Omega Bio-Tek)…

<<<<<<< HEAD

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genomic DNA Isolation - Olympia oyster adductor musle & mantle

2015

Olympia Oyster Genome Sequencing

DNA Isolation

DNA Quantification

E.Z.N.A. Mollusc Kit

gDNA

NanoDrop1000

olympia oyster

Ostrea lurida

Isolated gDNA from Ostrea lurida (Olympia oyster) adductor muscle & mantle samples collected by Brent & Steven on 20150812 using the E.Z.N.A Mollusc DNA Kit (Omega Bio-Tek)…

<<<<<<< HEAD

The system was previously set to use Steven’s Comcast SMTP server. Sending a test email from Eagle failed, indicating authentication failure. I changed this to use the…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Server Email Notifications Fix - Eagle

2015

Computer Servicing

Eagle

server

Synology

The system was previously set to use Steven’s Comcast SMTP server. Sending a test email from Eagle failed, indicating authentication failure. I changed this to use the…

<<<<<<< HEAD

Isolated gDNA from Panopea generosa (geoduck) adductor muscle & foot samples collected by Brent & Steven on 20150811 using the E.Z.N.A Mollusc DNA Kit (Omega Bio-Tek)…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genomic DNA Isolation - Geoduck Adductor Muscle & Foot

2015

Geoduck Genome Sequencing

adductor muscle

DNA Isolation

DNA Quantification

E.Z.N.A. Mollusc Kit

foot

gDNA

geoduck

NanoDrop1000

Panopea generosa

Aug 28, 2015

Isolated gDNA from Panopea generosa (geoduck) adductor muscle & foot samples collected by Brent & Steven on 20150811 using the E.Z.N.A Mollusc DNA Kit (Omega Bio-Tek)…

<<<<<<< HEAD

Aug 28, 2015

A box with the above title was established in the -20C in FTR 209 containing the following:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RAD-Seq Library Prep Reagents

2015

2bRAD Library Tests for Sequencing at Genewiz

Reagent Prep

AlfI

RAD-seq

Aug 19, 2015

A box with the above title was established in the -20C in FTR 209 containing the following:

<<<<<<< HEAD

Aug 19, 2015

Prepared sterile, ~1.5mL aliquots of SsoFast EvaGreen Supermix (received 20150810) in 2.0mL screw cap tubes. All aliquots were dated and stored @ -20C in the “PCR Supplies”…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

SsoFast EvaGreen Supermix Aliquots

2015

Reagent Prep

SsoFast EvaGreen Supermix

Aug 11, 2015

Prepared sterile, ~1.5mL aliquots of SsoFast EvaGreen Supermix (received 20150810) in 2.0mL screw cap tubes. All aliquots were dated and stored @ -20C in the “PCR Supplies”…

<<<<<<< HEAD

Aug 11, 2015

Performed reverse transcription on the Olympia oyster DNased RNA from the 1hr post-mechanical stress samples from Jake’s project. To accommodate the large numbers of…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Reverse Transcription – O.lurida DNased RNA 1hr post-mechanical stress

2015

Olympia oyster reciprocal transplant

cDNA

ctenidia

DNased RNA

gill

mechanical stress

olympia oyster

Ostrea lurida

reverse transcriptase

reverse transcription

Performed reverse transcription on the Olympia oyster DNased RNA from the 1hr post-mechanical stress samples from Jake’s project. To accommodate the large numbers of…

<<<<<<< HEAD

Ran qPCR on DNased RNA from earlier today to assess whether there was any residual gDNA after the DNase treatment with Oly_Actin_F/R primers (SR IDs: 1505, 1504).

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Jake's O.lurida ctenidia 1hr post-mechanical stress DNased RNA

2015

Olympia oyster reciprocal transplant

actin

ctenidia

DNased RNA

gill

mechanical stress

olympia oyster

Opticon2

Ostrea lurida

qPCR

'SR ID: 1504'

'SR ID: 1505'

SsoFast EvaGreen Supermix

`Aug 6, 2015`{=html}

DNased RNA from 20150727 was quantified using the Roberts Lab NanoDrop1000.

<<<<<<< HEAD

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Quantification - O.lurida 1hr post-mechanical heat stress DNased RNA

2015

Olympia oyster reciprocal transplant

ctenidia

DNased RNA

gill

mechanical stress

NanoDrop1000

olympia oyster

Ostrea lurida

RNA quantification

DNased RNA from 20150727 was quantified using the Roberts Lab NanoDrop1000.

<<<<<<< HEAD

RNA has been isolated and DNased from Jake’s mechanically stressed samples.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Goals - August 2015

2015

Goals

Aug 3, 2015

RNA has been isolated and DNased from Jake’s mechanically stressed samples.

<<<<<<< HEAD

Aug 3, 2015

Submitted a plate of purified PCR products (PCR products prepared by Jake on 20150625) that Jake set up 20150625, to the UW High-Throughput Genomics Center for Sanger…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Sample Submission – Olympia oyster PCRs Sanger Sequencing

2015

Olympia oyster reciprocal transplant

Samples Submitted

Submitted a plate of purified PCR products (PCR products prepared by Jake on 20150625) that Jake set up 20150625, to the UW High-Throughput Genomics Center for Sanger…

<<<<<<< HEAD

We had our first true test of the Synology RAID redundancy with our Synology 1812+ server (Owl). One of the hard drives (HDD) failed. All of the other drives were fine, the…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Server HDD Failure - Owl

2015

Computer Servicing

hard drive

HDD

owl

server

Synology

We had our first true test of the Synology RAID redundancy with our Synology 1812+ server (Owl). One of the hard drives (HDD) failed. All of the other drives were fine, the…

<<<<<<< HEAD

Quantified the RNA I isolated from Jake’s samples on 20150716 using the Roberts Lab NanoDrop1000 (ThermoFisher).

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNase Treatment - O.lurida Ctenidia 1hr Post-Mechanical Stress RNA

2015

Olympia oyster reciprocal transplant

ctenidia

DNase

gill

NanoDrop1000

olympia oyster

Ostrea lurida

RNA

RNA quantification

Turbo DNA-free

Jul 27, 2015

Quantified the RNA I isolated from Jake’s samples on 20150716 using the Roberts Lab NanoDrop1000 (ThermoFisher).

<<<<<<< HEAD

Jul 27, 2015

Isolated RNA from Jake’s Ostrea lurida ctenidia samples that had been subjected to mechanical stress (from 20150422).

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation – O.lurida Ctenidia 1hr Post-Mechanical Stress

2015

Olympia oyster reciprocal transplant

ctenidia

gill

mechanical stress

olympia oyster

Ostrea lurida

RNA isolation

RNAzol RT

Jul 15, 2015

Isolated RNA from Jake’s Ostrea lurida ctenidia samples that had been subjected to mechanical stress (from 20150422).

<<<<<<< HEAD

Jul 15, 2015

Isolated RNA from Jake’s Ostrea lurida ctenidia samples that had been subjected to mechanical stress (from 20150422).

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation - O.lurida Ctenidia 1hr Post-Mechanical Stress

2015

Olympia oyster reciprocal transplant

ctenidia

gill

mechanical stress

olympia oyster

Ostrea lurida

RNA

RNA isolation

RNAzol RT

Isolated RNA from Jake’s Ostrea lurida ctenidia samples that had been subjected to mechanical stress (from 20150422).

<<<<<<< HEAD

Prepared sterile, 1.0mL aliquots of SsoFast EvaGreen Supermix (received today) in 2.0mL screw cap tubes. All aliquots were dated and stored @ -20C in the “PCR Supplies” box.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

SsoFast EvaGreen Supermix Aliquots

2015

Reagent Prep

Prepared sterile, 1.0mL aliquots of SsoFast EvaGreen Supermix (received today) in 2.0mL screw cap tubes. All aliquots were dated and stored @ -20C in the “PCR Supplies” box.

<<<<<<< HEAD

I’ve been tweaking a shell script (notebook_backups.sh) to use the shell program wget to retrieve fully functional HTML versions of our online notebooks for offline viewing.…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Automatic Notebook Backups - wget Script & Synology Task Scheduler

2015

Computer Servicing

backup

script

Synology

wget

I’ve been tweaking a shell script (notebook_backups.sh) to use the shell program wget to retrieve fully functional HTML versions of our online notebooks for offline viewing.…

<<<<<<< HEAD

Ran a PCR to obtain luciferase DNA for sequencing.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

PCR - Sea Pen luciferase

2015

Apex Red Master Mix

gDNA

gel

luciferase

O'GeneRuler 100bp DNA ladder

PCR

Renilla reniformis

sea pen

`Jul 2, 2015`{=html}

Before we check out this month’s goals, let’s have a quick review of last month’s goals and which, if any, I was able to accomplish:

<<<<<<< HEAD

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

GOALS - July 2015

2015

Goals

Before we check out this month’s goals, let’s have a quick review of last month’s goals and which, if any, I was able to accomplish:

<<<<<<< HEAD

Jake and Steven recently noticed localized “hot spots” on most of Jake’s recent qPCRs, where higher levels of fluorescence were consistently showing up in interior portions…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Opticon2 Calibration

2015

calibration

FAM

Opticon

Opticon2

qPCR

troubleshooting

Jake and Steven recently noticed localized “hot spots” on most of Jake’s recent qPCRs, where higher levels of fluorescence were consistently showing up in interior portions…

<<<<<<< HEAD

Received notification that the samples sent on 20150601 for RNAseq were completed.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNAseq Data Receipt - Geoduck Gonad RNA 100bp PE Illumina

2015

Protein expression profiles during sexual maturation in Geoduck

geoduck

Geo_pool_F

Geo_pool_M

gonad

Illumina

Panopea generosa

RNA-seq

Data Received

Received notification that the samples sent on 20150601 for RNAseq were completed.

<<<<<<< HEAD

Submitted a plate of purified PCR products (PCR products prepared by Jake on 20150623) that Jake set up yesterday, to the UW High-Throughput Genomics Centerfor Sanger…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Sample Submission – Olympia oyster PCRs Sanger Sequencing

2015

HTGC

olympia oyster

Ostrea lurida

PCR

Sanger sequencing

Samples Submitted

Jun 25, 2015

Submitted a plate of purified PCR products (PCR products prepared by Jake on 20150623) that Jake set up yesterday, to the UW High-Throughput Genomics Centerfor Sanger…

<<<<<<< HEAD

Jun 25, 2015

Performed reverse transcription on the Olympia oyster DNased RNA from the control samples and the 1hr heat shock samples of Jake’s project. To accommodate the large numbers…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Reverse Transcription - O.lurida DNased RNA Controls and 1hr Heat Shock

2015

DNased RNA

M-MLV

oligo dT

olympia oyster

Ostrea lurida

reverse transcription

Jun 17, 2015

Performed reverse transcription on the Olympia oyster DNased RNA from the control samples and the 1hr heat shock samples of Jake’s project. To accommodate the large numbers…

<<<<<<< HEAD

Jun 17, 2015

Prepared two DNA plates and corresponding primer plates for sequencing at the UW HTGC from the purified gel-purified PCRs from yesterday. Primer plates were prepared by…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Sample Submission – Olympia oyster & Sea Pen PCRs Sanger Sequencing

2015

olympia oyster

Ostrea lurida

Renilla reniformis

Sanger sequencing

sea pen

Sample Submitted

Jun 16, 2015

Prepared two DNA plates and corresponding primer plates for sequencing at the UW HTGC from the purified gel-purified PCRs from yesterday. Primer plates were prepared by…

<<<<<<< HEAD

Jun 16, 2015

Purified DNA from the remaining PCR bands excised by Jake on 20150609 and 20150610, as well as Jonathan’s sea pen PCRs from 20150604 (previously avaiable in…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Gel Purification - Olympia Oyster and Sea Pen PCRs

2015

DNA

gel purification

olympia oyster

Ostrea lurida

PCR

Renilla reniformis

sea pen

Ultrafree-DA

Jun 15, 2015

Purified DNA from the remaining PCR bands excised by Jake on 20150609 and 20150610, as well as Jonathan’s sea pen PCRs from 20150604 (previously avaiable in…

<<<<<<< HEAD

Jun 15, 2015

Submitted a plate of purified PCR products (PCR products prepared by Jake on 20150609 and 20150610) that Jake set up yesterday, to the UW High-Throughput Genomics Center for…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Sample Submission - Olympia oyster PCRs Sanger Sequencing

2015

HTGC

olympia oyster

Ostrea lurida

PCR

Sanger sequencing

Samples Submitted

Jun 12, 2015

Submitted a plate of purified PCR products (PCR products prepared by Jake on 20150609 and 20150610) that Jake set up yesterday, to the UW High-Throughput Genomics Center for…

<<<<<<< HEAD

Jun 12, 2015

Prepared two pools of geoduck RNA for RNA-seq (Illumina HiSeq2500, 100bp, PE) with GENEWIZ, Inc.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Sample Submission - Geoduck Gonad for RNA-seq

2015

Protein expression profiles during sexual maturation in Geoduck

DNased RNA

geoduck

Geo_pool_F

Geo_pool_M

gonad

HiSeq2500

Illumina

Panopea generosa

RNA-seq

Samples Submitted

Prepared two pools of geoduck RNA for RNA-seq (Illumina HiSeq2500, 100bp, PE) with GENEWIZ, Inc.

<<<<<<< HEAD

Before we check out this month’s goals, let’s have a quick review of last month’s goals and which, if any, I was able to accomplish.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Goals - June 2015

2015

Goals

Before we check out this month’s goals, let’s have a quick review of last month’s goals and which, if any, I was able to accomplish.

<<<<<<< HEAD

Before proceeding with transcriptomics for this project, we need to assess the integrity of the RNA via Bioanalyzer.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Bioanalyzer - Geoduck Gonad RNA Quality Assessment

2015

Protein expression profiles during sexual maturation in Geoduck

bioanalyzer

DNased RNA

electropherogram

gel

geoduck

gonad

NanoDrop1000

Panopea generosa

May 27, 2015

Before proceeding with transcriptomics for this project, we need to assess the integrity of the RNA via Bioanalyzer.

<<<<<<< HEAD

May 27, 2015

Currently don’t have sufficient reagents to perform reverse transcription on the entire set of DNased RNA (control O.lurida ctenidia samples). To enable Jake to start…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Reverse Transcription - Subset of Jake’s O.lurida DNased RNA

2015

cDNA

ctenidia

DNased RNA

gill

heat shock

M-MLV

oligo dT

olympia oyster

Ostrea lurida

reverse transcriptase

reverse transcription

Currently don’t have sufficient reagents to perform reverse transcription on the entire set of DNased RNA (control O.lurida ctenidia samples). To enable Jake to start…

<<<<<<< HEAD

Previously trimmed the first 39 bases of sequence from reads from the BS-Seq data in an attempt to improve our ability to map the reads back to the C.gigas genome. However…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Bioinformatics – Trimmomatic/FASTQC on C.gigas Larvae OA NGS Data

2015

Crassostrea gigas larvae OA (2011) bisulfite sequencing

bioinformatics

BS-seq

Crassostrea gigas

FASTQC

Illumina

ipython notebook

jupyter notebook

NGS sequencing

Pacific oyster

Trimmomatic

Previously trimmed the first 39 bases of sequence from reads from the BS-Seq data in an attempt to improve our ability to map the reads back to the C.gigas genome. However…

<<<<<<< HEAD

The following DNased RNA samples showed inconsistencies between qPCR reps (one rep showed amplification, the other rep did not) on 20150515:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Re-run Jake's O.lurida DNased RNA Samples NC1, SC1, SC2, SC4 from 20150514

2015

actin

DNased RNA

olympia oyster

Opticon

Opticon2

Ostrea lurida

qPCR

'SR ID: 1504'

'SR ID: 1505'

SsoFast EvaGreen Supermix

`May 21, 2015`{=html}

Ran qPCR on DNased RNA from earlier today to assess whether there was any residual gDNA after the DNase treatment with Oly_Actin_F/R primers (SR IDs: 1505, 1504).

<<<<<<< HEAD

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR – Jake's O.lurida ctenidia DNased RNA (1hr Heat Shock Samples)

2015

actin

ctenidia

DNased RNA

gill

olympia oyster

Opticon

Opticon2

Ostrea lurida

qPCR

'SR ID: 1504'

'SR ID: 1505'

SsoFast EvaGreen Supermix

`May 14, 2015`{=html}

Ran qPCR on DNased RNA from earlier today to assess whether there was any residual gDNA after the DNase treatment with Oly_Actin_F/R primers (SR IDs: 1505, 1504).

<<<<<<< HEAD

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR – Jake's O.lurida ctenidia DNased RNA (Control Samples)

2015

actin

ctenidia

DNased RNA

gill

olympia oyster

Ostrea lurida

qPCR

'SR ID: 1504'

'SR ID: 1505'

SsoFast EvaGreen Supermix

`May 14, 2015`{=html}

Since the O.lurida RNA I isolated on 20150507 showed residual gDNA via qPCR, I treated 1.5μg of RNA from each sample using the Turbo DNA-free Kit (Ambion/Life Technologies)…

<<<<<<< HEAD

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNase Treatment - Jake’s O.lurida Ctenidia RNA (1hr Heat Shock) from 20150506

2015

DNase

DNased RNA

NanoDrop1000

olympia oyster

Ostrea lurida

RNA

RNA quantification

Turbo DNA-free

Since the O.lurida RNA I isolated on 20150507 showed residual gDNA via qPCR, I treated 1.5μg of RNA from each sample using the Turbo DNA-free Kit (Ambion/Life Technologies)…

<<<<<<< HEAD

Since the O.lurida RNA I isolated on 20150507 showed residual gDNA via qPCR, I treated 5μg of RNA from each sample using the Turbo DNA-free Kit (Ambion/Life Technologies)…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNase Treatment - Jake’s O.lurida Ctenidia RNA (Controls) from 20150507

2015

DNase

DNased RNA

NanoDrop1000

olympia oyster

Ostrea lurida

RNA

RNA quantification

Turbo DNA-free

Since the O.lurida RNA I isolated on 20150507 showed residual gDNA via qPCR, I treated 5μg of RNA from each sample using the Turbo DNA-free Kit (Ambion/Life Technologies)…

<<<<<<< HEAD

Since many newer computers are coming without optical disc drives (including my laptop, which I want to install this software on), I created an .iso disc image of the…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

ISO Creation - OpticonMonitor3 Disc Cloning

2015

Computer Servicing

Apple

disk image

ISO

Opticon

OS X

software

Since many newer computers are coming without optical disc drives (including my laptop, which I want to install this software on), I created an .iso disc image of the…

<<<<<<< HEAD

Ran qPCRs on the O.lurida total RNA I isolated on 20150507 to assess presence of gDNA carryover with Oly Actin primers (SR IDs: 1505, 1504).

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Jake O.lurida ctenidia RNA (Heat Shock Samples) from 20150506

2015

actin

ctenidia

gill

heat shock

olympia oyster

Opticon2

Ostrea lurida

qPCR

RNA

'SR ID: 1504'

'SR ID: 1505'

`May 12, 2015`{=html}

Ran qPCRs on the O.lurida total RNA I isolated on 20150507 to assess presence of gDNA carryover with Oly Actin primers (SR IDs: 1505, 1504).

<<<<<<< HEAD

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Jake O.lurida ctenidia RNA (Control Samples) From 20150507

2015

actin

ctenidia

gill

olympia oyster

Opticon2

Ostrea lurida

qPCR

RNA

'SR ID: 1504'

'SR ID: 1505'

`May 12, 2015`{=html}

UPDATE 20150528: The RNA isolated in this notebook entry may have been consolidated on 20150528.

<<<<<<< HEAD

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation – Geoduck Gonad in Paraffin Histology Blocks

2015

Protein expression profiles during sexual maturation in Geoduck

DNased RNA

geoduck

gonad

histology cassettes

NanoDrop1000

Panopea generosa

paraffin

PAXgene Tissue RNA Kit

RNA

RNA isolation

RNA quantification

UPDATE 20150528: The RNA isolated in this notebook entry may have been consolidated on 20150528.

<<<<<<< HEAD

Isolated RNA from Jake’s Olympia oyster ctenidia, controls, collected on 20150422. Samples had been homogenized and stored @ -80C.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation – Jake’s O. lurida Ctenidia Control from 20150422

2015

ctenidia

gill

heat shock

NanoDrop1000

olympia oyster

Ostrea lurida

RNA

RNA isolation

RNA quantification

RNAzol RT

Isolated RNA from Jake’s Olympia oyster ctenidia, controls, collected on 20150422. Samples had been homogenized and stored @ -80C.

<<<<<<< HEAD

In another troubleshooting attempt for this problematic BS-seq Illumina data, I’m going to use Trimmomatic to remove the first 39 bases of each read. This is due to the fact…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Bioinformatics - Trimmomatic/FASTQC on C.gigas Larvae OA NGS Data

2015

Crassostrea gigas larvae OA (2011) bisulfite sequencing

bioinformatics

BS-seq

Crassostrea gigas

FASTQC

graphs

ipython notebook

jupyter notebook

Pacific oyster

Trimmomatic

troubleshooting

In another troubleshooting attempt for this problematic BS-seq Illumina data, I’m going to use Trimmomatic to remove the first 39 bases of each read. This is due to the fact…

<<<<<<< HEAD

Isolated RNA from Jake’s Olympia oyster ctenidia, 1hr heat shock, collected on 20150422. Samples had been homogenized and stored @ -80C.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation - Jake’s O. lurida Ctenidia 1hr Heat Stress from 20150422

2015

ctenidia

DEPC-H2O

gill

heat shock

NanoDrop1000

olympia oyster

Ostrea lurida

pics

RNA isolation

RNA quantification

RNAzol RT

Isolated RNA from Jake’s Olympia oyster ctenidia, 1hr heat shock, collected on 20150422. Samples had been homogenized and stored @ -80C.

<<<<<<< HEAD

UPDATE 20150528: The RNA isolated in this notebook entry may have been consolidated on 20150528.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation – Geoduck Gonad in Paraffin Histology Blocks

2015

Protein expression profiles during sexual maturation in Geoduck

geoduck

histology cassettes

NanoDrop1000

Panopea generosa

paraffin

PAXgene Tissue RNA Kit

RNA isolation

RNA quantification

May 5, 2015

UPDATE 20150528: The RNA isolated in this notebook entry may have been consolidated on 20150528.

<<<<<<< HEAD

May 5, 2015

In an attempt to figure out what’s going on with the Illumina data we recently received for these samples, I BLASTed the 400ppm data set that had previously been de-novo asse…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

BLAST - C.gigas Larvae OA Illumina Data Against GenBank nt DB

2015

Crassostrea gigas larvae OA (2011) bisulfite sequencing

bioinformatics

BLAST

BLASTn

BS-seq

Crassostrea gigas

GenBank

ipython notebook

jupyter notebook

NCBI

Pacific oyster

May 4, 2015

In an attempt to figure out what’s going on with the Illumina data we recently received for these samples, I BLASTed the 400ppm data set that had previously been de-novo asse…

<<<<<<< HEAD

May 4, 2015

Here are the things I plan to tackle throughout the month of May:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Goals - May 2015

2015

Crassostrea gigas larvae OA (2011) bisulfite sequencing

Goals

Lineage-specific DNA methylation patterns in developing oysters

LSU C.virginica Oil Spill MBD BS Sequencing

Protein expression profiles during sexual maturation in Geoduck

BS-seq

Crassostrea gigas

Crassostrea virginica

Eastern oyster

geoduck

Pacific oyster

Panopea generosa

May 1, 2015

Here are the things I plan to tackle throughout the month of May:

<<<<<<< HEAD

May 1, 2015

In an attempt to figure out what’s going on with the Illumina data we recently received for these samples, I BLASTed the 400ppm data set that had previously been de-novo asse…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

BLASTN - C.gigas OA Larvae to C.gigas Ensembl 1.24 BLAST DB

2015

Crassostrea gigas larvae OA (2011) bisulfite sequencing

BLAST

Crassostrea gigas

ipython notebook

jupyter notebook

Pacific oyster

Apr 29, 2015

In an attempt to figure out what’s going on with the Illumina data we recently received for these samples, I BLASTed the 400ppm data set that had previously been de-novo asse…

<<<<<<< HEAD

Apr 29, 2015

UPDATE 20150528: The RNA isolated in this notebook entry may have been consolidated on 20150528.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation – Geoduck Gonad in Paraffin Histology Blocks

2015

Protein expression profiles during sexual maturation in Geoduck

geoduck

gonad

histology cassettes

Panopea generosa

paraffin

PAXgene Tissue RNA Kit

RNA isolation

RNA quantification

Apr 26, 2015

UPDATE 20150528: The RNA isolated in this notebook entry may have been consolidated on 20150528.

<<<<<<< HEAD

Apr 26, 2015

I received the Bioanalyzer data back for the geoduck foot RNA samples I submitted 20150422. The two samples were run on the RNA Pico chip assay.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Bioanalyzer Data - Geoduck RNA from Histology Blocks

2015

Protein expression profiles during sexual maturation in Geoduck

bioanalyzer

electropherogram

foot

gel

geoduck

Panopea generosa

RNA

RNA Pico

Apr 24, 2015

I received the Bioanalyzer data back for the geoduck foot RNA samples I submitted 20150422. The two samples were run on the RNA Pico chip assay.

<<<<<<< HEAD

Apr 24, 2015

UPDATE 20150528: The RNA isolated in this notebook entry may have been consolidated on 20150528.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation – Geoduck Gonad in Paraffin Histology Blocks

2015

Protein expression profiles during sexual maturation in Geoduck

DNased RNA

geoduck

gonad

histology cassettes

NanoDrop1000

Panopea generosa

PAXgene Tissue RNA Kit

RNA isolation

RNA quantification

Apr 23, 2015

UPDATE 20150528: The RNA isolated in this notebook entry may have been consolidated on 20150528.

<<<<<<< HEAD

Apr 23, 2015

Submitted 3μL (~75ng) of RNA from each of the two gonad samples isolated from foot tissue embedded in paraffin histology blocks 20150409 (to assess quality of RNA) to Jesse…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Bioanalyzer Submission - Geoduck Gonad RNA from Histology Blocks

2015

Protein expression profiles during sexual maturation in Geoduck

bioanalyzer

geoduck

gonad

Panopea generosa

paraffin

RNA

Apr 22, 2015

Submitted 3μL (~75ng) of RNA from each of the two gonad samples isolated from foot tissue embedded in paraffin histology blocks 20150409 (to assess quality of RNA) to Jesse…

<<<<<<< HEAD

Apr 22, 2015

Jupyter (IPython) Notebook: 20150414_C_gigas_Larvae_OA_Trimmomatic_FASTQC.ipynb

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Quality Trimming - C.gigas Larvae OA BS-Seq Data

2015

Crassostrea gigas larvae OA (2011) bisulfite sequencing

bioinformatics

BS-seq

Crassostrea gigas

FASTQC

ipython notebook

jupyter notebook

larvae

ocean acidification

Pacific oyster

Trimmomatic

Jupyter (IPython) Notebook: 20150414_C_gigas_Larvae_OA_Trimmomatic_FASTQC.ipynb

<<<<<<< HEAD

Jupyter (IPython) Notebook: 20150414_C_virginica_LSU_Oil_Spill_Trimmomatic_FASTQC.ipynb

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Quality Trimming - LSU C.virginica Oil Spill MBD BS-Seq Data

2015

LSU C.virginica Oil Spill MBD BS Sequencing

BS-seq

Crassostrea virginica

Eastern oyster

FASTQC

ipython notebook

jupyter notebook

MBD-Seq

NGS sequencing

oil

Trimmomatic

Jupyter (IPython) Notebook: 20150414_C_virginica_LSU_Oil_Spill_Trimmomatic_FASTQC.ipynb

<<<<<<< HEAD

Performed some rudimentary data analysis on the new, demultiplexed data downloaded earlier today:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Sequence Data Analysis - LSU C.virginica Oil Spill MBD BS-Seq Data

2015

LSU C.virginica Oil Spill MBD BS Sequencing

BS-seq

Crassostrea virginica

Eastern oyster

FASTQC

LSU

MBD-Seq

NGS sequencing

oil

Performed some rudimentary data analysis on the new, demultiplexed data downloaded earlier today:

<<<<<<< HEAD

Compared total amount of data generated from each index. The commands below send the output of the ‘ls -l’ command to awk. Awk sums the file sizes, found in the 5th field…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Sequence Data Analysis - C.gigas Larvae OA BS-Seq Data

2015

Crassostrea gigas larvae OA (2011) bisulfite sequencing

BS-seq

Crassostrea gigas

FASTQC

larvae

NGS sequencing

ocean acidification

Pacific oyster

Compared total amount of data generated from each index. The commands below send the output of the ‘ls -l’ command to awk. Awk sums the file sizes, found in the 5th field…

<<<<<<< HEAD

I had previously contacted Doug Turnbull at the Univ. of Oregon Genomics Core Facility for help demultiplexing this data, as it was initially returned to us as a single data…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Sequence Data - C.gigas OA Larvae BS-Seq Demultiplexed

2015

Crassostrea gigas larvae OA (2011) bisulfite sequencing

BS-seq

Crassostrea gigas

larvae

NGS sequencing

ocean acidification

Pacific oyster

I had previously contacted Doug Turnbull at the Univ. of Oregon Genomics Core Facility for help demultiplexing this data, as it was initially returned to us as a single data…

<<<<<<< HEAD

I had previously contacted Doug Turnbull at the Univ. of Oregon Genomics Core Facility for help demultiplexing this data, as it was initially returned to us as a single data…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Sequence Data - LSU C.virginica Oil Spill MBD BS-Seq Demultiplexed

2015

LSU C.virginica Oil Spill MBD BS Sequencing

BS-seq

Crassostrea virginica

Eastern oyster

LSU

MBD-Seq

NGS sequencing

oil

I had previously contacted Doug Turnbull at the Univ. of Oregon Genomics Core Facility for help demultiplexing this data, as it was initially returned to us as a single data…

<<<<<<< HEAD

Isolated RNA from geoduck gonad previously preserved with the PAXgene Tissue Fixative and Stabilizer and then embedded in paraffin blocks. See Grace’s notebook for full…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation - Geoduck Gonad in Paraffin Histology Blocks

2015

Protein expression profiles during sexual maturation in Geoduck

Disruptor Genie

geoduck

gonad

histology

histology cassettes

NanoDrop1000

Panopea generosa

paraffin

PAXgene Tissue RNA Kit

RNA isolation

RNA quantification

Apr 8, 2015

Isolated RNA from geoduck gonad previously preserved with the PAXgene Tissue Fixative and Stabilizer and then embedded in paraffin blocks. See Grace’s notebook for full…

<<<<<<< HEAD

Apr 8, 2015

Our sequencing data (Illumina HiSeq2500, 100SE) for this project has completed by Univ. of Oregon Genomics Core Facility(order number 2212).

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Sequencing Data - C.gigas Larvae OA

2015

Crassostrea gigas larvae OA (2011) bisulfite sequencing

BS-seq

checksum

code

Crassostrea gigas

curl

HiSeq2500

larvae

md5

ocean acidification

Pacific oyster

Mar 19, 2015

Our sequencing data (Illumina HiSeq2500, 100SE) for this project has completed by Univ. of Oregon Genomics Core Facility(order number 2212).

<<<<<<< HEAD

Mar 19, 2015

Before contacting the Univ. of Oregon facility for help with this sequence demultiplexing dilemma, I contacted Epigentek to find out what the other adaptor sequence that is…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Epinext Adaptor 1 Counts - LSU C.virginica Oil Spill Samples

2015

LSU C.virginica Oil Spill MBD BS Sequencing

Mar 17, 2015

Before contacting the Univ. of Oregon facility for help with this sequence demultiplexing dilemma, I contacted Epigentek to find out what the other adaptor sequence that is…

<<<<<<< HEAD

Mar 17, 2015

Initial analysis, comparing barcode identification methods, revealed the following info about demultiplexing on untrimmed sequences:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

TruSeq Adaptor Counts – LSU C.virginica Oil Spill Sequences

2015

LSU C.virginica Oil Spill MBD BS Sequencing

Mar 16, 2015

Initial analysis, comparing barcode identification methods, revealed the following info about demultiplexing on untrimmed sequences:

<<<<<<< HEAD

Mar 16, 2015

We recently received Illumina HiSeq2500 data back from this project. Initially looking at the data, something seems off. Using FASTQC, the quality drops of drastically…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

TruSeq Adaptor Identification Method Comparison - LSU C.virginica Oil Spill Sequences

2015

LSU C.virginica Oil Spill MBD BS Sequencing

barcodes

Crassostrea virginica

Eastern oyster

FASTQ

FASTQC

fastx_barcode_splitter

grep

index sequences

ipython notebook

jupyter notebook

TruSeq

Mar 14, 2015

We recently received Illumina HiSeq2500 data back from this project. Initially looking at the data, something seems off. Using FASTQC, the quality drops of drastically…

<<<<<<< HEAD

Mar 14, 2015

In an attempt to obtain the most accurate measurement of Claire’s sheared, heat shock mantle DNA, I quantified the samples using a third method: fluorescence.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Quantification - Claire’s C.gigas Sheared DNA

2015

Lineage-specific DNA methylation patterns in developing oysters

Crassostrea gigas

DNA Quantification

heat shock

Pacific oyster

Quant-iT DNA BR Kit

Mar 3, 2015

In an attempt to obtain the most accurate measurement of Claire’s sheared, heat shock mantle DNA, I quantified the samples using a third method: fluorescence.

<<<<<<< HEAD

Mar 3, 2015

Ran the 400ppm library preps on a DNA1000 Assay Chip (Agilent) on the Agilent 2100 Bioanalyzer.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Library Quality Assessment - C.gigas OA larvae Illumina libraries

2015

Crassostrea gigas larvae OA (2011) bisulfite sequencing

bioanalyzer

BS-seq

Crassostrea gigas

EpiNext Post-Bisulfite DNA Library Preparation Kit

Genomics Core Facility

larvae

library prep

ocean acidification

Pacific oyster

University of Oregon

Mar 2, 2015

Ran the 400ppm library preps on a DNA1000 Assay Chip (Agilent) on the Agilent 2100 Bioanalyzer.

<<<<<<< HEAD

Mar 2, 2015

Pooled 200ng each of the sheared 1B1 (4μL) & 1B2 (used the entire sample, 20μL) 5.13.11 1000ppm C.gigas larvae DNA samples for a total of 400ng. Total volume = 24μL.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

BS-seq Library Prep - C.gigas Larvae OA 1000ppm

2015

Crassostrea gigas larvae OA (2011) bisulfite sequencing

bisulfite conversion

BS-seq

Crassostrea gigas

EpiNext Post-Bisulfite DNA Library Preparation Kit

larvae

library prep

Methylamp DNA Modification

NanoDrop1000

ocean acidification

Pacific oyster

Feb 27, 2015

Pooled 200ng each of the sheared 1B1 (4μL) & 1B2 (used the entire sample, 20μL) 5.13.11 1000ppm C.gigas larvae DNA samples for a total of 400ng. Total volume = 24μL.

<<<<<<< HEAD

Feb 27, 2015

After the discovery that there wasn’t any DNA in the BS-seq Illumina library prep and no DNA in the bisulfite-treated DNA pool, I decided to try to recover any residual DNA…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Quantification - C.gigas Larvae 1000ppm

2015

Crassostrea gigas larvae OA (2011) bisulfite sequencing

Crassostrea gigas

DNA

larvae

NanoDrop1000

ocean acidification

Pacific oyster

After the discovery that there wasn’t any DNA in the BS-seq Illumina library prep and no DNA in the bisulfite-treated DNA pool, I decided to try to recover any residual DNA…

<<<<<<< HEAD

I previously checked Claire’s sheared DNA on the Bioanalyzer to verify the fragment size and to quantify the samples. Looking at her notebook, her numbers differ greatly…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Quantification - Claire’s Sheared C.gigas Mantle Heat Shock Samples

2015

Lineage-specific DNA methylation patterns in developing oysters

Crassostrea gigas

DNA Quantification

graphs

heat shock

mantle

NanoDrop1000

Pacific oyster

I previously checked Claire’s sheared DNA on the Bioanalyzer to verify the fragment size and to quantify the samples. Looking at her notebook, her numbers differ greatly…

<<<<<<< HEAD

To complement MBD ChiP-seq data and RNA-seq data that we have from this experiment, we want to generate, at a minimum, some BS-seq data from the same C.gigas individuals…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Bioanalyzer - C.gigas Sheared DNA from 20140108

2015

Lineage-specific DNA methylation patterns in developing oysters

bioanalyzer

Crassostrea gigas

DNA

DNA1000

electropherogram

heat shock

mantle

Pacific oyster

spreadsheet

Feb 20, 2015

To complement MBD ChiP-seq data and RNA-seq data that we have from this experiment, we want to generate, at a minimum, some BS-seq data from the same C.gigas individuals…

<<<<<<< HEAD

Feb 20, 2015

The completed BS Illumina library made on Friday (1000ppm) was quantified via fluorescence using the Quant-iT DNA BR Kit (Life Technologies/Invitrogen). Also quantified Jake…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Library Prep - Quantification of C.gigas larvae OA 1000ppm library

2015

Crassostrea gigas larvae OA (2011) bisulfite sequencing

BS-seq

Crassostrea gigas

DNA Quantification

FLx800 plate reader

larvae

library prep

ocean acidification

Pacific oyster

Quant-iT DNA BR Kit

The completed BS Illumina library made on Friday (1000ppm) was quantified via fluorescence using the Quant-iT DNA BR Kit (Life Technologies/Invitrogen). Also quantified Jake…

<<<<<<< HEAD

Our sequencing data (Illumina HiSeq2500, 100SE) for this project has completed by Univ. of Oregon Genomics Core Facility (order number 2112).

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Sequencing Data - LSU C.virginica MBD BS-Seq

2015

LSU C.virginica Oil Spill MBD BS Sequencing

BS-seq

checksum

code

Crassostrea virginica

curl

Eastern oyster

HiSeq2500

LSU

MBD

md5

oil

Data Received

Our sequencing data (Illumina HiSeq2500, 100SE) for this project has completed by Univ. of Oregon Genomics Core Facility (order number 2112).

<<<<<<< HEAD

The previous attempt at constructing a library for the 1000ppm larvae samples failed. I had previously sheared, quantified, and concentrated the DNA from this sample. As I…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Bisulfite NGS Library Prep - Bisulfite Conversion & Illumina Library Construction of C.gigas larvae DNA

2015

Crassostrea gigas larvae OA (2011) bisulfite sequencing

bisulfite conversion

BS-seq

Crassostrea gigas

DNA

larvae

library prep

ocean acidification

Pacific oyster

Feb 6, 2015

The previous attempt at constructing a library for the 1000ppm larvae samples failed. I had previously sheared, quantified, and concentrated the DNA from this sample. As I…

<<<<<<< HEAD

Feb 6, 2015

The two completed BS Illumina libraries (400ppm and 1000ppm) were quantified via fluorescence using the Quant-iT DNA BR Kit (Life Technologies/Invitrogen). Used 1uL of …

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Bisuflite NGS Library Prep – C.gigas larvae OA bisulfite library quantification

2015

Crassostrea gigas larvae OA (2011) bisulfite sequencing

BS-seq

Crassostrea gigas

DNA Quantification

FLx800 plate reader

library prep

ocean acidification

Pacific oyster

Quant-iT DNA BR Kit

Jan 28, 2015

The two completed BS Illumina libraries (400ppm and 1000ppm) were quantified via fluorescence using the Quant-iT DNA BR Kit (Life Technologies/Invitrogen). Used 1uL of …

<<<<<<< HEAD

Jan 28, 2015

Continued Illumina library prep of bisulfite-treated DNA samples (400ppm and 1000ppm; from 20150115) with Methylamp DNA Modification Kit (Epigentek) (PDF). Performed bead…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Bisuflite NGS Library Prep - C.gigas larvae OA bisulfite DNA (continued from yesterday)

2015

Crassostrea gigas larvae OA (2011) bisulfite sequencing

barcodes

BS-seq

Crassostrea gigas

library prep

Pacific oyster

Jan 27, 2015

Continued Illumina library prep of bisulfite-treated DNA samples (400ppm and 1000ppm; from 20150115) with Methylamp DNA Modification Kit (Epigentek) (PDF). Performed bead…

<<<<<<< HEAD

Jan 27, 2015

The two pooled bisulfite-treated DNA samples (400ppm and 1000ppm) from 20150115 were used to prepare bisulfite Illumina libraries with EpiNext Post-Bisulfite DNA Library…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Bisuflite NGS Library Prep - C.gigas larvae OA bisulfite DNA

2015

Crassostrea gigas larvae OA (2011) bisulfite sequencing

Crassostrea gigas

larvae

library prep

Methylamp DNA Modification

ocean acidification

Pacific oyster

Jan 26, 2015

The two pooled bisulfite-treated DNA samples (400ppm and 1000ppm) from 20150115 were used to prepare bisulfite Illumina libraries with EpiNext Post-Bisulfite DNA Library…

<<<<<<< HEAD

Jan 26, 2015

I was contacted by the sequencing facility at the University of Oregon regarding a sample quality issue with our library. As evidenced by the electropherogram below, there…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Library Cleanup - LSU C.virginica MBD BS Library

2015

LSU C.virginica Oil Spill MBD BS Sequencing

bioanalyzer

Crassostrea virginica

DNA Quantification

Eastern oyster

electropherogram

library prep

Jan 22, 2015

I was contacted by the sequencing facility at the University of Oregon regarding a sample quality issue with our library. As evidenced by the electropherogram below, there…

<<<<<<< HEAD

Jan 22, 2015

After discussing with Steven, decided to use only samples from 20110513, due to high algae amounts present in the 20110519 samples.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Bisulfite Conversion - C.gigas larvae OA Sheared DNA

2015

Crassostrea gigas larvae OA (2011) bisulfite sequencing

bisulfite conversion

DNA

Jan 14, 2015

After discussing with Steven, decided to use only samples from 20110513, due to high algae amounts present in the 20110519 samples.

<<<<<<< HEAD

Jan 14, 2015

The DNA extracted and sheared on 20150109 was in a volume too great to proceed with bisulfite conversion. Dried the samples to complete dryness in a SpeedVac (~4hrs). …

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

SpeedVac - C.gigas larvae OA DNA

2015

Crassostrea gigas larvae OA (2011) bisulfite sequencing

concentrate

Crassostrea gigas

DNA

SpeedVac

Jan 12, 2015

The DNA extracted and sheared on 20150109 was in a volume too great to proceed with bisulfite conversion. Dried the samples to complete dryness in a SpeedVac (~4hrs). …

<<<<<<< HEAD

Jan 12, 2015

Some tubes contained a high quantity of algae, based on quantity of material in tube and overall green color.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Isolation - C.gigas larvae from 2011 NOAA OA Experiment

2015

Crassostrea gigas larvae OA (2011) bisulfite sequencing

Crassostrea gigas

DNA Isolation

DNA Quantification

DNA Shearing

larvae

ocean acidification

Jan 9, 2015

Some tubes contained a high quantity of algae, based on quantity of material in tube and overall green color.

<<<<<<< HEAD

Jan 9, 2015

Combined the following libraries in equal quantities (17ng each) to create a single, multiplexed sample for sequencing (LSU_Oil_01):

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Bisulfite NGS Library - LSU C.virginica Oil Spill MBD Bisulfite DNA Sequencing Submission

2014

LSU C.virginica Oil Spill MBD BS Sequencing

Dec 22, 2014

Combined the following libraries in equal quantities (17ng each) to create a single, multiplexed sample for sequencing (LSU_Oil_01):

<<<<<<< HEAD

Dec 22, 2014

Continued library prep from yesterday. Set up Library Amplification according to the protocol. The samples received the following Barcode Indices:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Bisulfite NGS Library Prep - LSU C.virginica Oil Spill MBD Bisulfite DNA and Emma’s C.gigas Larvae OA Bisulfite DNA (continued from yesterday)

2014

Crassostrea gigas larvae OA (2011) bisulfite sequencing

LSU C.virginica Oil Spill MBD BS Sequencing

Dec 18, 2014

Continued library prep from yesterday. Set up Library Amplification according to the protocol. The samples received the following Barcode Indices:

<<<<<<< HEAD

Dec 18, 2014

Constructed next generation libraries (Illumina) using the bisulfite-treated DNA from yesterday using the EpiNext Post-Bisulfite DNA Library Preparation Kit - Illumina…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Bisulfite NGS Library Prep - LSU C.virginica Oil Spill Bisulfite DNA and Emma’s C.gigas Larvae OA Bisulfite DNA

2014

Crassostrea gigas larvae OA (2011) bisulfite sequencing

LSU C.virginica Oil Spill MBD BS Sequencing

Dec 17, 2014

Constructed next generation libraries (Illumina) using the bisulfite-treated DNA from yesterday using the EpiNext Post-Bisulfite DNA Library Preparation Kit - Illumina…

<<<<<<< HEAD

Dec 17, 2014

Performed bisulfite conversion on MBD DNA samples from LSU C.virginica oil spill samples (see 201411202 and 20141126) and Emma’s C.gigas larvae OA DNA samples (see 20141121)…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Bisulfite Conversion - LSU C.virginica Oil Spill MBD DNA and Emma’s C.gigas Larvae OA DNA

2014

Crassostrea gigas larvae OA (2011) bisulfite sequencing

LSU C.virginica Oil Spill MBD BS Sequencing

Dec 16, 2014

Performed bisulfite conversion on MBD DNA samples from LSU C.virginica oil spill samples (see 201411202 and 20141126) and Emma’s C.gigas larvae OA DNA samples (see 20141121)…

<<<<<<< HEAD

Dec 16, 2014

Due to poor “tag counts” from the initial sequencing (DATE) and the re-sequencing (20131127) of this sample, the HTGU facility has concluded that the library is probably at…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Isolation - Claire’s C.gigas Female Gonad for Illumina Bisulfite Sequencing

2014

Lineage-specific DNA methylation patterns in developing oysters

Dec 11, 2014

Due to poor “tag counts” from the initial sequencing (DATE) and the re-sequencing (20131127) of this sample, the HTGU facility has concluded that the library is probably at…

<<<<<<< HEAD

Dec 11, 2014

Precipitation was continued according to the MethylMiner Methylated DNA Enrichment Kit (Invitrogen). Since I will need sample volumes of 24uL for the subsequent bisulfite…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

EtOH Precipitation - LSU C.virginica Oil Spill MBD Continued (from 20141126)

2014

LSU C.virginica Oil Spill MBD BS Sequencing

Dec 2, 2014

Precipitation was continued according to the MethylMiner Methylated DNA Enrichment Kit (Invitrogen). Since I will need sample volumes of 24uL for the subsequent bisulfite…

<<<<<<< HEAD

Dec 2, 2014

Enrichment was performed using the MethylMiner Methylated DNA Enrichment Kit (Invitrogen) according to the manufacturer’s protocol with the following changes:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Methylated DNA Enrichment (MBD) - LSU C.virginica Oil Spill gDNA

2014

LSU C.virginica Oil Spill MBD BS Sequencing

Nov 26, 2014

Enrichment was performed using the MethylMiner Methylated DNA Enrichment Kit (Invitrogen) according to the manufacturer’s protocol with the following changes:

<<<<<<< HEAD

Nov 26, 2014

Used the remainder of the “sheared” samples (see today’s earlier entry; ~2750ng). Brought the volumes up to 80uL and transferred to 0.5mL snap cap tubes. The volume of 80uL…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Shearing - LSU C.virginica Oil Spill gDNA

2014

LSU C.virginica Oil Spill MBD BS Sequencing

Used the remainder of the “sheared” samples (see today’s earlier entry; ~2750ng). Brought the volumes up to 80uL and transferred to 0.5mL snap cap tubes. The volume of 80uL…

<<<<<<< HEAD

Ran ~250ng (out of 3000ng, according to Claire) of LSU C.virginica oil spill gDNA on a gel that was previously sheared by Claire to verify that shearing was successful.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Gel - Sheared gDNA

2014

LSU C.virginica Oil Spill MBD BS Sequencing

Ran ~250ng (out of 3000ng, according to Claire) of LSU C.virginica oil spill gDNA on a gel that was previously sheared by Claire to verify that shearing was successful.

<<<<<<< HEAD

Shipped (dry ice) ~15ug of total RNA from each of the following samples to Genewiz, Inc for high throughput transcriptomic sequencing (Illumina HiSeq2500, 100bp, single end).

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Seq - C.gigas Total RNA from Claire’s Pre/Post Heat Shock

2014

Samples Submitted

Nov 24, 2014

Shipped (dry ice) ~15ug of total RNA from each of the following samples to Genewiz, Inc for high throughput transcriptomic sequencing (Illumina HiSeq2500, 100bp, single end).

<<<<<<< HEAD

Nov 24, 2014

Isolated gDNA using DNazol from the following larval samples for potential MBD selection and bisulfite sequencing:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Isolation - C.gigas Larvae from Emma OA Experiments

2014

Crassostrea gigas larvae OA (2011) bisulfite sequencing

Nov 21, 2014

Isolated gDNA using DNazol from the following larval samples for potential MBD selection and bisulfite sequencing:

<<<<<<< HEAD

Nov 21, 2014

Prepared 10nM of the library in total volume of 20uL of Buffer EB (Qiagen) + 0.1% Tween-20, according the University of Oregon’s Genomic’s Core.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RAD Sequencing - Oly Oyster gDNA-01 RAD Library (from 20141110)

2014

Olympia oyster reciprocal transplant

Samples Submitted

library prep

olympia oyster

Ostrea lurida

RAD-seq

Nov 17, 2014

Prepared 10nM of the library in total volume of 20uL of Buffer EB (Qiagen) + 0.1% Tween-20, according the University of Oregon’s Genomic’s Core.

<<<<<<< HEAD

Nov 17, 2014

Quantified the library using the Quant-It BR Kit (Life Technologies) according to the manufacturer’s protocol. Only used 1uL of the RAD library due to the small volume (15uL).

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Quantification - Oly Oyster gDNA-01 RAD Library

2014

Olympia oyster reciprocal transplant

Nov 10, 2014

Quantified the library using the Quant-It BR Kit (Life Technologies) according to the manufacturer’s protocol. Only used 1uL of the RAD library due to the small volume (15uL).

<<<<<<< HEAD

Nov 10, 2014

Used gel-purified, size-selected DNA from yesterday to prepare the RAD library using the Kappa LTP Kit:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Library Prep - Oly Oyster gDNA-01 RAD

2014

Olympia oyster reciprocal transplant

Nov 7, 2014

Used gel-purified, size-selected DNA from yesterday to prepare the RAD library using the Kappa LTP Kit:

<<<<<<< HEAD

Nov 7, 2014

Pooled “low quality” samples and pooled “high quality” samples separately (in 1.5mL snap cap tubes) prior to shearing to improve chances of getting similar DNA size ranges.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Shearing & Size Selection - Oly Oyster gDNA RAD P1 Adapters (from 20141105)

2014

Olympia oyster reciprocal transplant

Nov 6, 2014

Pooled “low quality” samples and pooled “high quality” samples separately (in 1.5mL snap cap tubes) prior to shearing to improve chances of getting similar DNA size ranges.

<<<<<<< HEAD

Nov 6, 2014

Made 25nM working stock from the 100nM stock adapter plate provided by Carita. Added 2uL of each adapter to corresponding well of SbfI digested DNA (e.g. DNA plate well A1…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Ligation - Illumina P1 Adapters for Oly Oyster gDNA-01 RAD Sequencing (from 20141031)

2014

Olympia oyster reciprocal transplant

Nov 5, 2014

Made 25nM working stock from the 100nM stock adapter plate provided by Carita. Added 2uL of each adapter to corresponding well of SbfI digested DNA (e.g. DNA plate well A1…

<<<<<<< HEAD

Nov 5, 2014

Samples required two days of drying for all samples to fully dry down.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Restriction Digest - Oly Oyster gDNA-01 for RAD Sequencing (from 20141029)

2014

Olympia oyster reciprocal transplant

Oct 31, 2014

Samples required two days of drying for all samples to fully dry down.

<<<<<<< HEAD

Oct 31, 2014

Transferred 500ng of gDNA from each sample to a 96-well, low-profile, non-skirted PCR plate (sample layout matches that of the layout of the source gDNA plate) and air-dried…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Allocation - Oly Oyster gDNA-01 for RAD Sequencing (from 20141022)

2014

Olympia oyster reciprocal transplant

Oct 29, 2014

Transferred 500ng of gDNA from each sample to a 96-well, low-profile, non-skirted PCR plate (sample layout matches that of the layout of the source gDNA plate) and air-dried…

<<<<<<< HEAD

Oct 29, 2014

Quantified the gDNA isolated 20141014 using the Quant-iT dsDNA Broad Range kit (Life Technologies).

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Quantification - Oly Oyster gDNA-01 for RAD Sequencing (from 20141014)

2014

Olympia oyster reciprocal transplant

Oct 22, 2014

Quantified the gDNA isolated 20141014 using the Quant-iT dsDNA Broad Range kit (Life Technologies).

<<<<<<< HEAD

Oct 22, 2014

Olympia oysters from three different Puget Sound locations/populations (HL, NF, and SN) were collected and stored @ -80C on 8/29/2103.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Isolation - Olympia Oyster Populations for RAD Sequencing

2014

Olympia oyster reciprocal transplant

Oct 14, 2014

Olympia oysters from three different Puget Sound locations/populations (HL, NF, and SN) were collected and stored @ -80C on 8/29/2103.

<<<<<<< HEAD

Oct 14, 2014

Oyster (C.virginica) gill samples exposed to “no oil” and “highest level of oil.” Samples were stored in Rack #2 in the -80C. Images of the box label and included paperwork…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Package - Received Package from Jerome LaPeyre from LSU

2014

LSU C.virginica Oil Spill MBD BS Sequencing

Sep 26, 2014

Oyster (C.virginica) gill samples exposed to “no oil” and “highest level of oil.” Samples were stored in Rack #2 in the -80C. Images of the box label and included paperwork…

<<<<<<< HEAD

Sep 26, 2014

Since the previous isolation attempt was unsuccessful (see 20140922), we’re trying a slightly different approach than yesterday.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Isolation - C.gigas Larvae from Katie Latterhos

2014

Miscellaneous

Sep 23, 2014

Since the previous isolation attempt was unsuccessful (see 20140922), we’re trying a slightly different approach than yesterday.

<<<<<<< HEAD

Sep 23, 2014

Isolated gDNA from two C.gigas larvae samples (stored in RNA Later) from Katie Latterhos:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Isolation - C.gigas Larvae from Katie Latterhos and Emma

2014

Miscellaneous

Sep 22, 2014

Isolated gDNA from two C.gigas larvae samples (stored in RNA Later) from Katie Latterhos:

<<<<<<< HEAD

Sep 22, 2014

Realized that the PCR performed on 20140828 used the incorrect forward primer! As such, am repeating as before, but with the correct forward primer:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

PCR - Mac’s Bisulfite-Treated DNA

2014

Miscellaneous

Sep 3, 2014

Realized that the PCR performed on 20140828 used the incorrect forward primer! As such, am repeating as before, but with the correct forward primer:

<<<<<<< HEAD

Sep 3, 2014

Per Mac’s request, ran a PCR on a set of bisulfite-treated DNA (in her gDNA 2014 box in small -20C):

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

PCR - Mac’s Bisulfite-Treated DNA

2014

Miscellaneous

Aug 28, 2014

Per Mac’s request, ran a PCR on a set of bisulfite-treated DNA (in her gDNA 2014 box in small -20C):

<<<<<<< HEAD

Aug 28, 2014

Received RNA-seq data from Cornell. They provided a convenient download script for retrieving all the data files at one time (a bash script containing a series of wget…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA-Seq - Sea Star Data Download

2014

Sea star RNA-seq

May 28, 2014

Received RNA-seq data from Cornell. They provided a convenient download script for retrieving all the data files at one time (a bash script containing a series of wget…

<<<<<<< HEAD

May 28, 2014

Isolated RNA from the following samples provided by Jessica Blanchette (stored in RNA later):

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation - Jessica’s Geoduck Larval Stages

2014

Miscellaneous

May 27, 2014

Isolated RNA from the following samples provided by Jessica Blanchette (stored in RNA later):

<<<<<<< HEAD

May 27, 2014

Isolated DNA from the following samples, provided by Mackenzie:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Isolation - Mackenzie’s C.gigas EE2 Gonad Samples

2014

Miscellaneous

May 16, 2014

Isolated DNA from the following samples, provided by Mackenzie:

<<<<<<< HEAD

May 16, 2014

Sent the following samples (in their entirety) to Cornell for Illumina HiSeq 100bp paired-end sequencing:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Sample Submission - Colleen Sea Star (Pycnopodia) Coelomycete RNA for Illumina Sequencing

2014

Samples Submitted

Sea star RNA-seq

May 14, 2014

Sent the following samples (in their entirety) to Cornell for Illumina HiSeq 100bp paired-end sequencing:

<<<<<<< HEAD

May 14, 2014

Apparently the Bio26 sample provided on 20140428 was incorrect. Instead, the sample should have been CF26.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation - Colleen Sea Star (Pycnopodia) Coelomycete Sample

2014

Sea star RNA-seq

May 8, 2014

Apparently the Bio26 sample provided on 20140428 was incorrect. Instead, the sample should have been CF26.

<<<<<<< HEAD

May 8, 2014

Isolated RNA from the following samples (provided by Colleen Burge):

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation - Colleen Sea Star (Pycnopodia) Coelomycete Samples

2014

Sea star RNA-seq

Apr 28, 2014

Isolated RNA from the following samples (provided by Colleen Burge):

<<<<<<< HEAD

Apr 28, 2014

Trying this sample again(!!), but will now use TE for pellet resuspension to prevent sample degradation. Incubated sample RT on rotator in 500uL of DNazol + 2.7uL of…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Isolation - Claire’s C.gigas Female Gonad

2014

Lineage-specific DNA methylation patterns in developing oysters

Trying this sample again(!!), but will now use TE for pellet resuspension to prevent sample degradation. Incubated sample RT on rotator in 500uL of DNazol + 2.7uL of…

<<<<<<< HEAD

Performed an EtOH precipitation on the sea start RNA due to some residual column resin (?) in the tubes after elution.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Ethanol Precipitation - Colleen’s Sea Star Coelomycete RNA from Yesterday

2014

Sea star RNA-seq

Performed an EtOH precipitation on the sea start RNA due to some residual column resin (?) in the tubes after elution.

<<<<<<< HEAD

Zymoresearch support suggested putting the samples through another set of columns to help clean up the apparent phenol carryover that was seen (absorbance peak shifted to…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Clean Up - Colleen’s Sea Star Coelomycete RNA from 20140416

2014

Sea star RNA-seq

Apr 24, 2014

Zymoresearch support suggested putting the samples through another set of columns to help clean up the apparent phenol carryover that was seen (absorbance peak shifted to…

<<<<<<< HEAD

Apr 24, 2014

Isolated RNA from the following samples stored in RNAlater:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation - Colleens’ Sea Star Coelomycetes Samples

2014

Sea star RNA-seq

Isolated RNA from the following samples stored in RNAlater:

<<<<<<< HEAD

Due to the recent poor quality gDNA that has been isolated from C.gigas gonad, I decided to do a quick test using TE for DNA pellet resuspension in hopes that old Buffer EB…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Isolation - Test Sample

2014

Lineage-specific DNA methylation patterns in developing oysters

Miscellaneous

Due to the recent poor quality gDNA that has been isolated from C.gigas gonad, I decided to do a quick test using TE for DNA pellet resuspension in hopes that old Buffer EB…

<<<<<<< HEAD

Due to low 260/230 values and Mac’s smeary sample, performed a phenol-chloroform DNA cleanup on the samples isolated 20140410.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Phenol-Chloroform DNA Clean Up - Mac and Claire’s Samples (from 20140410)

2014

Lineage-specific DNA methylation patterns in developing oysters

Apr 14, 2014

Due to low 260/230 values and Mac’s smeary sample, performed a phenol-chloroform DNA cleanup on the samples isolated 20140410.

<<<<<<< HEAD

Apr 14, 2014

Isolated RNA from two samples stored in RNAlater that had either no visible pellet or a minutely visible pellet:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation - Sea Star Coelomocytes (from Colleen)

2014

Sea star RNA-seq

Isolated RNA from two samples stored in RNAlater that had either no visible pellet or a minutely visible pellet:

<<<<<<< HEAD

Due to the poor quality DNA yielded by the DNeasy Kit (Qiagen; see 20140404), I am re-isolating these samples using DNazol (Molecular Research Center). Weighed tissue from…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Isolation - Claire’s C.gigas Female Gonad and Mac’s C.gigas Gonad

2014

Lineage-specific DNA methylation patterns in developing oysters

Due to the poor quality DNA yielded by the DNeasy Kit (Qiagen; see 20140404), I am re-isolating these samples using DNazol (Molecular Research Center). Weighed tissue from…

<<<<<<< HEAD

Cloned the XP hard drive of the computer hooked up to the Opticon qPCR machine using Macrium Reflect Free. Verified that the clone is bootable and operates correctly. Will…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Cloned Hard Drive - Windows XP Opticon Computer (Aquacul8)

2014

Computer Servicing

Cloned the XP hard drive of the computer hooked up to the Opticon qPCR machine using Macrium Reflect Free. Verified that the clone is bootable and operates correctly. Will…

<<<<<<< HEAD

Ran out 2uL of Clair’es C.gigas female gonad gDNA (from 20140328) and Mac’s C.gigas gonad gDNA (from 20140402) for quality assessment. Both samples had been isolated using…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA gel - Claire’s C.gigas Female Gonad and Mac’s C.gigas Gonad

2014

Lineage-specific DNA methylation patterns in developing oysters

Ran out 2uL of Clair’es C.gigas female gonad gDNA (from 20140328) and Mac’s C.gigas gonad gDNA (from 20140402) for quality assessment. Both samples had been isolated using…

<<<<<<< HEAD

Tried another method of RNA Isolation for comparison with regular TriReagent method.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation - Sea Star Coelomocytes (provided by Colleen Burge)

2014

Sea star RNA-seq

Apr 2, 2014

Tried another method of RNA Isolation for comparison with regular TriReagent method.

<<<<<<< HEAD

Apr 2, 2014

Isolated RNA from the following samples (stored in RNAlater):

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation - Sea Star Coelomocytes (provided by Colleen Burge)

2014

Sea star RNA-seq

Isolated RNA from the following samples (stored in RNAlater):

<<<<<<< HEAD

Mac’s been having some difficulty getting good quality gDNA from some of her gonad samples, so she asked me to give it a shot.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Isolation - Mackenzie’s C.gigas Gonad Sample

2014

Miscellaneous

Mac’s been having some difficulty getting good quality gDNA from some of her gonad samples, so she asked me to give it a shot.

<<<<<<< HEAD

Isolated gDNA from Claire’s “Female DNA” (from 05/16/2013) using the Qiagen Blood & Tissue DNeasy Kit according to the manufacturer’s protocol, with the following changes:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Isolation - C.gigas Female Gonads (from frozen)

2014

Lineage-specific DNA methylation patterns in developing oysters

Mar 28, 2014

Isolated gDNA from Claire’s “Female DNA” (from 05/16/2013) using the Qiagen Blood & Tissue DNeasy Kit according to the manufacturer’s protocol, with the following changes:

<<<<<<< HEAD

Mar 28, 2014

We’ve had some Illumina sequencing issues with Yanouk’s samples, so I ran the samples out on a 0.8% agarose gel to evaluate the levels of degradation. Loaded 2uL of each…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Quality Check - Yanouk’s Oyster gDNA

2014

Miscellaneous

Mar 14, 2014

We’ve had some Illumina sequencing issues with Yanouk’s samples, so I ran the samples out on a 0.8% agarose gel to evaluate the levels of degradation. Loaded 2uL of each…

<<<<<<< HEAD

Mar 14, 2014

Isolated additional geoduck gDNA from the two fresh (now frozen) geoduck’s that Brent provided me with on 20140212 so that we can potentially isolate RNA from the same…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Isolation - Geoduck

2014

Miscellaneous

Feb 19, 2014

Isolated additional geoduck gDNA from the two fresh (now frozen) geoduck’s that Brent provided me with on 20140212 so that we can potentially isolate RNA from the same…

<<<<<<< HEAD

Feb 19, 2014

After speaking with Axa regarding the DNA concentrations, he would like the DNA from the ethanol-fixed tissue to be more concentrated, and he wants them in ddH2O instead of…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Precipitation - Geoduck DNA from 20140213

2014

Miscellaneous

Feb 18, 2014

After speaking with Axa regarding the DNA concentrations, he would like the DNA from the ethanol-fixed tissue to be more concentrated, and he wants them in ddH2O instead of…

<<<<<<< HEAD

Feb 18, 2014

Since yesterday’s DNA isolation failed to yield sufficient quantity of DNA from the ethanol-fixed samples, I isolated additional DNA from the same samples.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Isolation - Geoduck

2014

Miscellaneous

Feb 13, 2014

Since yesterday’s DNA isolation failed to yield sufficient quantity of DNA from the ethanol-fixed samples, I isolated additional DNA from the same samples.

<<<<<<< HEAD

Feb 13, 2014

Isolated gDNA from 6 geoduck siphon samples provided by Brent using the Qiagen DNeasy Spin Kit. Samples were as follows:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Isolation - Geoduck

2014

Miscellaneous

Feb 12, 2014

Isolated gDNA from 6 geoduck siphon samples provided by Brent using the Qiagen DNeasy Spin Kit. Samples were as follows:

<<<<<<< HEAD

Feb 12, 2014

Samples from yesterday were centrifuged 30mins, 4000g, 4C (fixed angle rotor).

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Gylcogen Assay - Emma’s C.gigas Whole Body Samples (continued from yesterday)

2013

Miscellaneous

Dec 7, 2013

Samples from yesterday were centrifuged 30mins, 4000g, 4C (fixed angle rotor).

<<<<<<< HEAD

Dec 7, 2013

Finally located the remaining half of Emma’s samples. These had already been freeze dried AND pulverized! So, I just had to weigh out ~half of each sample for the glycogen…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Gylcogen Assay - Emma’s C.gigas Whole Body Samples

2013

Miscellaneous

Dec 6, 2013

Finally located the remaining half of Emma’s samples. These had already been freeze dried AND pulverized! So, I just had to weigh out ~half of each sample for the glycogen…

<<<<<<< HEAD

Dec 6, 2013

Samples from yesterday were centrifuged 30mins, 4000g, 4C (fixed angle rotor).

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Gylcogen & Carboyhydrate Assays - Emma’s C.gigas Whole Body Samples (continued from yesterday)

2013

Miscellaneous

Nov 26, 2013

Samples from yesterday were centrifuged 30mins, 4000g, 4C (fixed angle rotor).

<<<<<<< HEAD

Nov 26, 2013

Samples were previously freeze dried overnight and stored @ -20C. To maximize sample homogeneity and, thus, increase accuracy of both assays, all samples were mechanically…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Gylcogen and Carboyhydrate Assays - Emma’s C.gigas Whole Body Samples

2013

Miscellaneous

Nov 25, 2013

Samples were previously freeze dried overnight and stored @ -20C. To maximize sample homogeneity and, thus, increase accuracy of both assays, all samples were mechanically…

<<<<<<< HEAD

Nov 25, 2013

Repeated PCR from 20130919, but with a newly designed reverse primer. Primers were designed using MethPrimer (SR IDs: 1553, 1555). Primers were designed using MethPrimer:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

PCR - Lake Trout C1q

2013

Miscellaneous

Oct 28, 2013

Repeated PCR from 20130919, but with a newly designed reverse primer. Primers were designed using MethPrimer (SR IDs: 1553, 1555). Primers were designed using MethPrimer:

<<<<<<< HEAD

Oct 28, 2013

Repeated PCR from 20130919, but with a newly designed set of primers that targets the desired region of C1q for sequencing (SR IDs: 1553, 1554). Primers were designed in…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

PCR - Lake Trout C1q

2013

Miscellaneous

Oct 10, 2013

Repeated PCR from 20130919, but with a newly designed set of primers that targets the desired region of C1q for sequencing (SR IDs: 1553, 1554). Primers were designed in…

<<<<<<< HEAD

Oct 10, 2013

Ran PCR on lake trout DNA and lake trout bisulfite-converted DNA. Used primers SRIDs: 1551 and 1552. DNA was isolated by Caroline Storer on 4/4/2011 and bisulfite converted…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Quantification - Yanouk’s DNA Samples

2013

Miscellaneous

<<<<<<< HEAD

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

PCR - Lake Trout C1q

2013

Miscellaneous

Sep 19, 2013

Ran PCR on lake trout DNA and lake trout bisulfite-converted DNA. Used primers SRIDs: 1551 and 1552. DNA was isolated by Caroline Storer on 4/4/2011 and bisulfite converted…

<<<<<<< HEAD

Sep 19, 2013

Performed PCR using the primers CG_HK_CDS_2132-2158 (SRID: 1521) and Cg_Hk_CDS_3’_no_stop (SRID: 1519) on pooled C.gigas cDNA (from DATE).

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

PCR - Hexokinase Partial CDS

2013

Miscellaneous

Apr 9, 2013

Performed PCR using the primers CG_HK_CDS_2132-2158 (SRID: 1521) and Cg_Hk_CDS_3’_no_stop (SRID: 1519) on pooled C.gigas cDNA (from DATE).

<<<<<<< HEAD

Apr 9, 2013

Performed PCR using newly designed primers to amplify the C. gigas hexokinase “promoter” (-2059bp from start) along with a portion of the first exon.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

PCR - Hexokinase and Partial Exon #1

2013

Miscellaneous

Apr 8, 2013

Performed PCR using newly designed primers to amplify the C. gigas hexokinase “promoter” (-2059bp from start) along with a portion of the first exon.

<<<<<<< HEAD

Apr 8, 2013

Performed a repeat of the failed PCR from 20130227, but used a pool of cDNA (made from 20110311 C.gigas cDNA) instead of a single sample and changed the annealing temp to 50C.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

PCR - Hexokinase Promoter and CDS (repeat from 20130227)

2013

Miscellaneous

Mar 14, 2013

Performed a repeat of the failed PCR from 20130227, but used a pool of cDNA (made from 20110311 C.gigas cDNA) instead of a single sample and changed the annealing temp to 50C.

<<<<<<< HEAD

Mar 14, 2013

Performed PCR to amplify the C.gigas hexokinase (ACCESSION#) promoter region (-2059bp) and the CDS without the stop codon. Elimination of the stop codon allows for…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

PCR - Hexokinase Promoter and CDS

2013

Miscellaneous

Feb 27, 2013

Performed PCR to amplify the C.gigas hexokinase (ACCESSION#) promoter region (-2059bp) and the CDS without the stop codon. Elimination of the stop codon allows for…

<<<<<<< HEAD

Feb 27, 2013

Performed an RT reaction on pooled herring gonad and liver mRNA from 20091026 for James Raymond at the UNLV. A single RT reaction was performed using 12.75uL (208ng) of the…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Reverse Transcription - Herring RNA from 20091026

2013

Miscellaneous

Feb 13, 2013

Performed an RT reaction on pooled herring gonad and liver mRNA from 20091026 for James Raymond at the UNLV. A single RT reaction was performed using 12.75uL (208ng) of the…

<<<<<<< HEAD

Feb 13, 2013

Ran qPCR on Halley’s cDNA to see if I could get them to work. She has been getting high levels of fluorescence at the initiation of the qPCR cycling that shouldn’t be there. …

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Halley cDNA Check

2012

Miscellaneous

Nov 28, 2012

Ran qPCR on Halley’s cDNA to see if I could get them to work. She has been getting high levels of fluorescence at the initiation of the qPCR cycling that shouldn’t be there. …

<<<<<<< HEAD

Nov 28, 2012

Reverse transcribed the class FISH441 RNA to cDNA. Followed protocol provided on the FISH441 Wiki page, NOT the usual Roberts Lab protocol, with some modifications.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Reverse Transcription - FISH441 RNA

2012

Miscellaneous

Nov 21, 2012

Reverse transcribed the class FISH441 RNA to cDNA. Followed protocol provided on the FISH441 Wiki page, NOT the usual Roberts Lab protocol, with some modifications.

<<<<<<< HEAD

Nov 21, 2012

Ran qPCR on manila clam larvae cDNA that Dave made on 8/7/2012, using the sample sets from 7/29/2011 and 8/5/2011 of the OA manila clam experiment he ran.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Manila Clam Larvae cDNA (from August 2012 - Dave’s Notebook)

2012

Miscellaneous

Ran qPCR on manila clam larvae cDNA that Dave made on 8/7/2012, using the sample sets from 7/29/2011 and 8/5/2011 of the OA manila clam experiment he ran.

<<<<<<< HEAD

Ran qPCR on manila clam larvae cDNA that Dave made on 8/7/2012, using the sample sets from 7/29/2011 and 8/5/2011 of the OA manila clam experiment he ran.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Manila Clam Larvae cDNA (from August 2012 - Dave’s Notebook)

2012

Miscellaneous

Ran qPCR on manila clam larvae cDNA that Dave made on 8/7/2012, using the sample sets from 7/29/2011 and 8/5/2011 of the OA manila clam experiment he ran.

<<<<<<< HEAD

Ran qPCR on manila clam larvae cDNA that Dave made on 8/7/2012, using the sample sets from 7/29/2011 and 8/5/2011 of the OA manila clam experiment he ran.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Manila Clam Larvae cDNA (from August 2012 - Dave’s Notebook)

2012

Miscellaneous

Ran qPCR on manila clam larvae cDNA that Dave made on 8/7/2012, using the sample sets from 7/29/2011 and 8/5/2011 of the OA manila clam experiment he ran.

<<<<<<< HEAD

Performed qPCR on Dave’s manila clam larvae DNased RNA from August 2012 using EF1a primers (SR IDs: 1463, 1474).

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - DNased Manila Clam Larvae RNA (from August 2012 - Dave’s Notebook)

2012

Miscellaneous

Oct 26, 2012

Performed qPCR on Dave’s manila clam larvae DNased RNA from August 2012 using EF1a primers (SR IDs: 1463, 1474).

<<<<<<< HEAD

Oct 26, 2012

Photos of oysters are here:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Received oysters from Taylor Shellfish.

2012

Miscellaneous

Oct 16, 2012

Photos of oysters are here:

<<<<<<< HEAD

Oct 16, 2012

Ran qPCR to test uniformity of Opticon 2, after it was serviced on 20120926.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Opticon Test

2012

Miscellaneous

Oct 10, 2012

Ran qPCR to test uniformity of Opticon 2, after it was serviced on 20120926.

<<<<<<< HEAD

Oct 10, 2012

Performed plasmid isolation on 17 bacterial cultures Emma inoculated yesterday using the QIAprep Spin Mini Kit (Qiagen) using ~1.4mL of culture according to the…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Minipreps - Emma’s Illumina Library Cloning

2012

Miscellaneous

Jul 23, 2012

Performed plasmid isolation on 17 bacterial cultures Emma inoculated yesterday using the QIAprep Spin Mini Kit (Qiagen) using ~1.4mL of culture according to the…

<<<<<<< HEAD

Jul 23, 2012

Took heat-fragmented RNA provided by Emma (see Emma’s Notebook, 7/3/2011) and proceeded to make first strand cDNA, as described in the Eli Meyer protocol for Illumina HiSeq . …

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Illumina RNAseq Library Construction - 32 C.gigas Individuals

2012

Crassostrea gigas

Illumina

library prep

Pacific oyster

RNA-seq

Took heat-fragmented RNA provided by Emma (see Emma’s Notebook, 7/3/2011) and proceeded to make first strand cDNA, as described in the Eli Meyer protocol for Illumina HiSeq . …

<<<<<<< HEAD

Reconstituted all of the oligos and barcodes for library construction in TE (pH = 8.0) to a final concentration of 100uM. Created 10uM working stocks of all oligos and…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Oligo Reconstitution - Illumina RNAseq Library Oligos and Barcodes

2012

Miscellaneous

Reconstituted all of the oligos and barcodes for library construction in TE (pH = 8.0) to a final concentration of 100uM. Created 10uM working stocks of all oligos and…

<<<<<<< HEAD

After submission of QPX samples to HTGU for Illumina library prep yesterday, I was notified that there was insufficient RNA for the QPX RNA samples. I checked the source RNA…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Chloroform Clean Up - Lexie’s QPX RNA from 20110504

2012

Miscellaneous

Jul 10, 2012

After submission of QPX samples to HTGU for Illumina library prep yesterday, I was notified that there was insufficient RNA for the QPX RNA samples. I checked the source RNA…

<<<<<<< HEAD

Jul 10, 2012

Submitted samples to HTGU for Illumina sequencing.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Sample Submission - QPX RNA and DNA for Illumina 36bp single-end RNA/DNAseq

2012

Miscellaneous

Samples Submitted

Jul 9, 2012

Submitted samples to HTGU for Illumina sequencing.

<<<<<<< HEAD

Jul 9, 2012

Pooling volumes/quantities for QPX RNA/DNA-seq: 20120705 Oly larvae and QPX HiSeq Calcs

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

QPX Sample Pooling for Illumina Sequencing

2012

Miscellaneous

Jul 6, 2012

Pooling volumes/quantities for QPX RNA/DNA-seq: 20120705 Oly larvae and QPX HiSeq Calcs

<<<<<<< HEAD

Jul 6, 2012

Ran qPCR with VtpA primers on cDNA and DNA (from yesterday) of C.gigas larvae to see levels of V.tubiashii compared to their water filter samples (see 20120326). Master mix…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Detection of V.tubiashii Presence and Expression Using VtpA Primers in DNA/cDNA from yesterday

2012

Miscellaneous

May 1, 2012

Ran qPCR with VtpA primers on cDNA and DNA (from yesterday) of C.gigas larvae to see levels of V.tubiashii compared to their water filter samples (see 20120326). Master mix…

<<<<<<< HEAD

May 1, 2012

Performed reverse transcription using random primers (Promega) diluted 1:100 (5ng/uL) with 175ng of DNased total RNA. Random primers were used because we will be targeting…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Reverse Transcription - DNased C.gigas Larval RNA from 20120427

2012

Miscellaneous

M-MLV

reverse transcription

RNA

Vibrio tubiashii

Apr 30, 2012

Performed reverse transcription using random primers (Promega) diluted 1:100 (5ng/uL) with 175ng of DNased total RNA. Random primers were used because we will be targeting…

<<<<<<< HEAD

Apr 30, 2012

Ran qPCR using V.tubiashii VtpA primers (from Elene; no SR ID). Used 0.5uL of each DNased RNA sample, which equals ~40ng of RNA, which would be the equivalent amount of RNA…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Check DNased RNA from Earlier Today for Residual gDNA

2012

CFX96

Crassostrea gigas

DNased RNA

larvae

Pacific oyster

qPCR

Vibrio tubiashii

VtpA

Ran qPCR using V.tubiashii VtpA primers (from Elene; no SR ID). Used 0.5uL of each DNased RNA sample, which equals ~40ng of RNA, which would be the equivalent amount of RNA…

<<<<<<< HEAD

Treated 5ug of total RNA (in a 50uL rxn) using Turbo DNA-free (Ambion) according to the “Standard” protocol. Samples were spec’d on the Roberts Lab NanoDrop 1000.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNase Treatment - C.gigas Larvae RNA from yesterday

2012

Miscellaneous

Treated 5ug of total RNA (in a 50uL rxn) using Turbo DNA-free (Ambion) according to the “Standard” protocol. Samples were spec’d on the Roberts Lab NanoDrop 1000.

<<<<<<< HEAD

Samples that had been split from earlier today (see the RNA Isolation below) were resuspended in 1mL of DNAzol (MRC). 100ug of Proteinase K (Fermentas) was added to each…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

gDNA Isolation - C.gigas Larvae from Taylor Summer 2011

2012

Miscellaneous

Samples that had been split from earlier today (see the RNA Isolation below) were resuspended in 1mL of DNAzol (MRC). 100ug of Proteinase K (Fermentas) was added to each…

<<<<<<< HEAD

Samples had been stored in RNA Later (Ambion). Samples were pelleted and the RNA Later supe removed. Samples were washed (2x) with 1mL TE (pH = 8.0) to remove excess salt…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation - C.gigas Larvae from Taylor Summer 2011

2012

Miscellaneous

Samples had been stored in RNA Later (Ambion). Samples were pelleted and the RNA Later supe removed. Samples were washed (2x) with 1mL TE (pH = 8.0) to remove excess salt…

<<<<<<< HEAD

Ran qPCR on the Taylor water filter DNA extracts from 20120322 using V.tubiashii VtpA primers (provide by Elene; no SR ID?) instead of 16s primers, which failed to produce…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Taylor Water Filter DNA Extracts from 20120322 - Sam White

2012

Miscellaneous

Mar 26, 2012

Ran qPCR on the Taylor water filter DNA extracts from 20120322 using V.tubiashii VtpA primers (provide by Elene; no SR ID?) instead of 16s primers, which failed to produce…

<<<<<<< HEAD

Mar 26, 2012

Repeated exactly what was done earlier today due to apparent contamination in negative controls.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Repeat of qPCR from Earlier Today

2012

Miscellaneous

Repeated exactly what was done earlier today due to apparent contamination in negative controls.

<<<<<<< HEAD

Ran qPCR on the Taylor water filter DNA extracts from yesterday using V.tubiashii 16s primers (SR IDs: 455, 456). Used RE22 DNA as a positive control, provided by Elene. Mast…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Taylor Water Filter DNA Extracts from Yesterday

2012

Miscellaneous

Ran qPCR on the Taylor water filter DNA extracts from yesterday using V.tubiashii 16s primers (SR IDs: 455, 456). Used RE22 DNA as a positive control, provided by Elene. Mast…

<<<<<<< HEAD

Extracted DNA from the following water filter samples using the Qiagen DNeasy Blood & Tissue Kit:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Extraction - Taylor Water Filter Samples from 2011

2012

Miscellaneous

Mar 22, 2012

Extracted DNA from the following water filter samples using the Qiagen DNeasy Blood & Tissue Kit:

<<<<<<< HEAD

Mar 22, 2012

Performed reverse transcription on 1.5ug of DNased RNA in a 75uL reaction, using oligo dT primers. All reagents were scaled appropriately (based on Promega’s M-MLV RT…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Reverse Transcription - Dave’s Manila Clam (Venerupis philippinarum) DNased RNA from 20120307 and 20120302

2012

Miscellaneous

Mar 12, 2012

Performed reverse transcription on 1.5ug of DNased RNA in a 75uL reaction, using oligo dT primers. All reagents were scaled appropriately (based on Promega’s M-MLV RT…

<<<<<<< HEAD

Mar 12, 2012

Performed qPCR on all DNased RNA samples from this group (samples #1-48) using beta actin primers (SR IDs: 1379, 1380). 0.5uL of each DNased RNA was used, which was the…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Dave’s Manila Calm (Venerupis philippinarum) DNased RNA from yesterday and 20120302

2012

Miscellaneous

Mar 8, 2012

Performed qPCR on all DNased RNA samples from this group (samples #1-48) using beta actin primers (SR IDs: 1379, 1380). 0.5uL of each DNased RNA was used, which was the…

<<<<<<< HEAD

Mar 8, 2012

Isolated RNA from Manila Clam gill samples provided by Dave, according to protocol. Samples were resuspended in 0.1%-DEPC H2O and spec’d on the Roberts Lab NanoDrop1000.…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation - Dave’s Manila Clam (Venerupis philippinarum) Gill Samples (#25-48)

2012

Miscellaneous

Mar 7, 2012

Isolated RNA from Manila Clam gill samples provided by Dave, according to protocol. Samples were resuspended in 0.1%-DEPC H2O and spec’d on the Roberts Lab NanoDrop1000.…

<<<<<<< HEAD

Mar 7, 2012

DNased RNA using Ambion’s Turbo DNA-free Kit following the “routine” protocol. 5ug of total RNA from each sample was treated in 50uL reactions. Samples will be spec’d on…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNase - Dave’s Manila Clam (Venerupis philippinarum) Gill RNA from Yesterday

2012

Miscellaneous

Mar 2, 2012

DNased RNA using Ambion’s Turbo DNA-free Kit following the “routine” protocol. 5ug of total RNA from each sample was treated in 50uL reactions. Samples will be spec’d on…

<<<<<<< HEAD

Mar 2, 2012

Isolated RNA from Manila Clam gill samples provided by Dave according to protocol. Samples were resuspended in 0.1%-DEPC H2O and spec’d on the Roberts Lab NanoDrop1000.…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation - Dave’s Manila Clam (Venerupis philippinarum) Gill Samples (#1-24)

2012

Miscellaneous

Mar 1, 2012

Isolated RNA from Manila Clam gill samples provided by Dave according to protocol. Samples were resuspended in 0.1%-DEPC H2O and spec’d on the Roberts Lab NanoDrop1000.…

<<<<<<< HEAD

Mar 1, 2012

Performed qPCR on all 12 samples. Used the following primers, provided by Elene, to detect V.tubiashii expression:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - cDNA from 20120208

2012

Miscellaneous

Feb 9, 2012

Performed qPCR on all 12 samples. Used the following primers, provided by Elene, to detect V.tubiashii expression:

<<<<<<< HEAD

Feb 9, 2012

Performed qPCR on all 12 samples. Used Cg_EF1aF/R2 (SR IDs: 1410 & 1412) for one set of qPCRs and Vtub_16s_F/R (SR IDs: 455 & 456) for the other set of qPCRs. Used pooled…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - cDNA from earlier today

2012

Miscellaneous

Performed qPCR on all 12 samples. Used Cg_EF1aF/R2 (SR IDs: 1410 & 1412) for one set of qPCRs and Vtub_16s_F/R (SR IDs: 455 & 456) for the other set of qPCRs. Used pooled…

<<<<<<< HEAD

Performed reverse transcription on Dnased RNA from 20120125 using 175ng RNA from each sample. Also used random primers (instead of the usual Oligo dT primers) since these…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Reverse Transcription - C.gigas larvae DNased RNA (from 20120125)

2012

Miscellaneous

Performed reverse transcription on Dnased RNA from 20120125 using 175ng RNA from each sample. Also used random primers (instead of the usual Oligo dT primers) since these…

<<<<<<< HEAD

Checked DNased RNA samples from earlier today for the presence of residual gDNA. Used C.gigas BB16 gDNA (from 20110201) diluted to ~7ng/uL as a positive control to match the…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - DNased RNA from earlier today

2012

Miscellaneous

Checked DNased RNA samples from earlier today for the presence of residual gDNA. Used C.gigas BB16 gDNA (from 20110201) diluted to ~7ng/uL as a positive control to match the…

<<<<<<< HEAD

5ug of each RNA was DNased using Ambion’s Turbo DNA-free Kit, according to the rigorous protocol and spec’d on Roberts Lab NanoDrop 1000. RNA volume calcs are here.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNAse - C.gigas RNA from 20120124

2012

Miscellaneous

5ug of each RNA was DNased using Ambion’s Turbo DNA-free Kit, according to the rigorous protocol and spec’d on Roberts Lab NanoDrop 1000. RNA volume calcs are here.

<<<<<<< HEAD

All of the RNA samples were re-combined with their respective counterparts and subject to a standard EtOH precipitation (0.1 volumes of 3M NaOAc, pH = 5.2, 2.5 volumes 100%…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation - C.gigas Larvae from 20110412 & 20110705 (Continued from 20120112)

2012

Miscellaneous

Jan 24, 2012

All of the RNA samples were re-combined with their respective counterparts and subject to a standard EtOH precipitation (0.1 volumes of 3M NaOAc, pH = 5.2, 2.5 volumes 100%…

<<<<<<< HEAD

Jan 24, 2012

RNA was isolated from C.gigas larvae collected from Taylor Shellfish hatchery on the dates noted above. Samples were in RNA Later. RNA Later was removed. Attempted…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation - C.gigas Larvae from 20110412 & 20110705

2012

Miscellaneous

Jan 12, 2012

RNA was isolated from C.gigas larvae collected from Taylor Shellfish hatchery on the dates noted above. Samples were in RNA Later. RNA Later was removed. Attempted…

<<<<<<< HEAD

Jan 12, 2012

Samples were submitted for sequencing to the University of Washington HTGU, two times from each direction using vector M13F/R primers. See Sequence Log for plate layout.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Sequencing - COX/PGS Clones from yesterday/today

2011

Miscellaneous

Oct 14, 2011

Samples were submitted for sequencing to the University of Washington HTGU, two times from each direction using vector M13F/R primers. See Sequence Log for plate layout.

<<<<<<< HEAD

Oct 14, 2011

Selected 10 colonies (1-8, 18, 28) for mini-preps. Inoculated 5mL 1x LB + 50ug/mL of Kanamycin. Incubated O/N, 37C, 200RPM. 3mL of each culture were used for mini-preps.…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Mini-preps - COX/PGS Cloning Colonies from today

2011

Miscellaneous

Selected 10 colonies (1-8, 18, 28) for mini-preps. Inoculated 5mL 1x LB + 50ug/mL of Kanamycin. Incubated O/N, 37C, 200RPM. 3mL of each culture were used for mini-preps.…

<<<<<<< HEAD

Performed PCR on 40 colonies using both qPCR primer sets to see if I could differentiate between which colonies potentially contained each isoform to reduce the amount of…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

PCR - COX/PGS Cloning Colony Screens from yesterday

2011

Miscellaneous

Performed PCR on 40 colonies using both qPCR primer sets to see if I could differentiate between which colonies potentially contained each isoform to reduce the amount of…

<<<<<<< HEAD

Cloned the purified “qPCR Fragment” from 20111006 using the TOPO TA Cloning Kit (Invitrogen). Performed a half reaction (total volume = 3uL), using 1uL of purified PCR…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Cloning - Purified COX/PGS “qPCR Fragment” from 20111006

2011

Miscellaneous

Oct 12, 2011

Cloned the purified “qPCR Fragment” from 20111006 using the TOPO TA Cloning Kit (Invitrogen). Performed a half reaction (total volume = 3uL), using 1uL of purified PCR…

<<<<<<< HEAD

Oct 12, 2011

Ran PCR using primers Cg_COX1/2_qPCR_F, Cg_COX1_qPCR_R, Cg_COX2_454align1_R (SR IDs: 1192, 1191, 1190; respectively). Template was pooled cDNA from 20110311 of various…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

PCR - Purified COX/PGS 1/2 DNA from earlier today

2011

Miscellaneous

Ran PCR using primers Cg_COX1/2_qPCR_F, Cg_COX1_qPCR_R, Cg_COX2_454align1_R (SR IDs: 1192, 1191, 1190; respectively). Template was pooled cDNA from 20110311 of various…

<<<<<<< HEAD

Ran PCR using primers Cg_COX_982_F and Cg_COX_2138_R (SR IDs: 1149 & 1151, respectively). Template was pooled cDNA from 20110311 of various C.gigas tissues. These primers…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

PCR - Region Outside of COX/PGS qPCR Primers

2011

Miscellaneous

Ran PCR using primers Cg_COX_982_F and Cg_COX_2138_R (SR IDs: 1149 & 1151, respectively). Template was pooled cDNA from 20110311 of various C.gigas tissues. These primers…

<<<<<<< HEAD

Performed an EtOH on gel-purified PCR products from 20110921. Briefly, added 0.1 vols of 3M sodium acetate (pH=5.2; 43uL), mixed and then added 2.5 vols of 100% EtOH…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Ethanol Precipitation - Full-length PGS1 cDNA (from 20110921)

2011

Miscellaneous

Sep 29, 2011

Performed an EtOH on gel-purified PCR products from 20110921. Briefly, added 0.1 vols of 3M sodium acetate (pH=5.2; 43uL), mixed and then added 2.5 vols of 100% EtOH…

<<<<<<< HEAD

Sep 29, 2011

Still have insufficient quantities of DNA for sequencing. Master mix calcs and cycling params are here. Additionally, used some of the purified PCR product as template in…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

PCR - Full-length PGS1 cDNA

2011

Miscellaneous

Still have insufficient quantities of DNA for sequencing. Master mix calcs and cycling params are here. Additionally, used some of the purified PCR product as template in…

<<<<<<< HEAD

Added 0.1 vols of 3M sodium acetate (pH = 5.2; 38uL) and 2 vols of 100% EtOH (836uL). Incubated 30mins @ -20C. Pelleted DNA 16,000g, 15mins, 4C. Removed supe. Washed pellet…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Ethanol Precipitation - Purified PGS1 PCR from yesterday

2011

Miscellaneous

Added 0.1 vols of 3M sodium acetate (pH = 5.2; 38uL) and 2 vols of 100% EtOH (836uL). Incubated 30mins @ -20C. Pelleted DNA 16,000g, 15mins, 4C. Removed supe. Washed pellet…

<<<<<<< HEAD

Need more PCR product for sequencing. Repeated reaction from 20110825.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

PCR - Full-length PGS1 cDNA

2011

Miscellaneous

Sep 20, 2011

Need more PCR product for sequencing. Repeated reaction from 20110825.

<<<<<<< HEAD

Sep 20, 2011

Repeated PCR from 20110825 to attempt to amplify the full-length cDNA for PGS2 (COX2), however this time using a more robust polymerase (Amplitaq Gold) in hopes of getting…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

PCR - Full-length PGS2 cDNA

2011

Miscellaneous

Sep 14, 2011

Repeated PCR from 20110825 to attempt to amplify the full-length cDNA for PGS2 (COX2), however this time using a more robust polymerase (Amplitaq Gold) in hopes of getting…

<<<<<<< HEAD

Sep 14, 2011

Ran PCR to amplify full-length cDNAs of PGS1 & PGS2 (COX1 & COX2) using primers designed to anneal in the 5’/3’UTRs of each isoform. PGS1 primers = SRIDs: 1377, 1378. PGS2…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

PCR - Full-length PGS1 & PGS2 cDNAs

2011

Miscellaneous

Aug 25, 2011

Ran PCR to amplify full-length cDNAs of PGS1 & PGS2 (COX1 & COX2) using primers designed to anneal in the 5’/3’UTRs of each isoform. PGS1 primers = SRIDs: 1377, 1378. PGS2…

<<<<<<< HEAD

Aug 25, 2011

Ran a qPCR using 3hr Vibrio vulnificus exposure cDNA from 20110311. Original experiment conducted on 20110111 with defensin primers (SR IDs: 1109 & 1070) and GAPDH (SR IDs…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - C.gigas V.vulnificus Exposure cDNA (from 20110311)

2011

cDNA

CFX96

Crassostrea gigas

defensin

GAPDH

Pacific oyster

qPCR

Vibrio exposure

Vibrio vulnificus

Aug 11, 2011

Ran a qPCR using 3hr Vibrio vulnificus exposure cDNA from 20110311. Original experiment conducted on 20110111 with defensin primers (SR IDs: 1109 & 1070) and GAPDH (SR IDs…

<<<<<<< HEAD

Aug 11, 2011

Used new primers for sequencing (SR IDs: 1351 & 1352) clone #4. Sequenced clone two times in each direction. DNA and primers were sent for sequencing at ASU. Requested “High…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Sequencing - C.gigas COX2/PGS2 Clone #4 from 20110728

2011

Miscellaneous

Aug 4, 2011

Used new primers for sequencing (SR IDs: 1351 & 1352) clone #4. Sequenced clone two times in each direction. DNA and primers were sent for sequencing at ASU. Requested “High…

<<<<<<< HEAD

Aug 4, 2011

Isolated plasmid DNA from 3mL of liquid cultures that were inoculated yesterday using Qiagen’s miniprep kit. DNA was eluted with 50uL of EB. DNA was prepped and sent for…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Plasmid Isolation & Sequencing - C.gigas COX2/PGS2 Clones (from yesterday)

2011

Miscellaneous

Jul 28, 2011

Isolated plasmid DNA from 3mL of liquid cultures that were inoculated yesterday using Qiagen’s miniprep kit. DNA was eluted with 50uL of EB. DNA was prepped and sent for…

<<<<<<< HEAD

Jul 28, 2011

Inoculated 4 x 5mL 1xLB + Kan50 with a colony from each set of clones, incubated 37C, 200RPM, O/N. Will mini prep and send for sequencing tomorrow.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Bacterial Cultures - C.gigas COX2/PGS2 Clones (from yesterday)

2011

Miscellaneous

Jul 27, 2011

Inoculated 4 x 5mL 1xLB + Kan50 with a colony from each set of clones, incubated 37C, 200RPM, O/N. Will mini prep and send for sequencing tomorrow.

<<<<<<< HEAD

Jul 27, 2011

Performed colony PCRs on the 4 sets of cloning reactions that were performed yesterday using the M13F/R vector primers. Colonies were picked, restreaked on a fresh LB Kan50…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Colony PCRs - C.gigas COX2/PGS2 Clones (from yesterday)

2011

Miscellaneous

Jul 26, 2011

Performed colony PCRs on the 4 sets of cloning reactions that were performed yesterday using the M13F/R vector primers. Colonies were picked, restreaked on a fresh LB Kan50…

<<<<<<< HEAD

Jul 26, 2011

The bands that were excised and purified earlier today were cloned in to pCR2.1 using the TOPO TA Cloning Kit (Invitrogen) according to the manufacturer’s protocol with the…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Cloning - C.gigas COX2/PGS2 5’/3’ RACE Products (from earlier today)

2011

Miscellaneous

The bands that were excised and purified earlier today were cloned in to pCR2.1 using the TOPO TA Cloning Kit (Invitrogen) according to the manufacturer’s protocol with the…

<<<<<<< HEAD

Performed nested RACE PCR on the RACE PCR products generated on 20110722 using the following nested primers: PGS2_ngspRACE_5’ (SR ID: 1350) and PGS2_ngspRACE_3’ (SR ID…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

5’/3’ RACE - C.gigas COX2/PGS2 Nested RACE PCR

2011

Miscellaneous

Performed nested RACE PCR on the RACE PCR products generated on 20110722 using the following nested primers: PGS2_ngspRACE_5’ (SR ID: 1350) and PGS2_ngspRACE_3’ (SR ID…

<<<<<<< HEAD

Additional RACE using gene specific primers (SR IDs: 1347 & 1348) for C.gigas COX2/PGS2 according to Clontech’s SMARTer cDNA RACE Kit protocol. 3’/5’ RACE cDNA libraries are…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

5’/3’ RACE - C.gigas COX2/PGS2 RACE PCR

2011

Miscellaneous

Jul 22, 2011

Additional RACE using gene specific primers (SR IDs: 1347 & 1348) for C.gigas COX2/PGS2 according to Clontech’s SMARTer cDNA RACE Kit protocol. 3’/5’ RACE cDNA libraries are…

<<<<<<< HEAD

Jul 22, 2011

Sent plasmid prep to ASU (5uL of plasmid + 1uL of 10uM M13F/R). SJW01 = M13F, SJW02 = M13R.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Sequencing - PGS Hi 4 (PGS2/COX2)

2011

Miscellaneous

Jul 15, 2011

Sent plasmid prep to ASU (5uL of plasmid + 1uL of 10uM M13F/R). SJW01 = M13F, SJW02 = M13R.

<<<<<<< HEAD

Jul 15, 2011

Plasmid was isolated from 3mL of liquid culture started yesterday using the Qiagen MiniPrep Kit, according to the manufacturer’s protocol. Will send off for sequencing.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Plasmid Isolation - Miniprep on PGS Hi 4 Colony from yesterday

2011

Miscellaneous

Jul 12, 2011

Plasmid was isolated from 3mL of liquid culture started yesterday using the Qiagen MiniPrep Kit, according to the manufacturer’s protocol. Will send off for sequencing.

<<<<<<< HEAD

Jul 12, 2011

Ran a colony PCR at the same time that I inoculated liquid cultures, using M13 primers.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

PCR - Colony PCR on Restreaked PGS2 Clones from 20110707

2011

Miscellaneous

Ran a colony PCR at the same time that I inoculated liquid cultures, using M13 primers.

<<<<<<< HEAD

Inoculated 5mL of 1xLB + Kan50 with re-streaked colonies from 20110707. Incubated O/N, 37C, 200RPM. Will isolated plasmids of those with inserts tomorrow.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Bacterial Cultures - Liquid Cultures of PGS2/COX2 Colonies from 20110707

2011

Miscellaneous

Inoculated 5mL of 1xLB + Kan50 with re-streaked colonies from 20110707. Incubated O/N, 37C, 200RPM. Will isolated plasmids of those with inserts tomorrow.

<<<<<<< HEAD

Sequencing of the PGS2/COX2 clone failed (was empty vector). Restreaked bacterial clones on to a Kan50 plate (made 20110413 by SJW) from a plate that Caroline Storer had…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Clone Restreaking - PGS2 Hi/Lo Clones (from 20110421)

2011

Miscellaneous

Jul 7, 2011

Sequencing of the PGS2/COX2 clone failed (was empty vector). Restreaked bacterial clones on to a Kan50 plate (made 20110413 by SJW) from a plate that Caroline Storer had…

<<<<<<< HEAD

Jul 7, 2011

Ran a qPCR on all cDNA samples. Created a standard curve to possibly allow for use of the BioRad software for gene expression analysis. Standard curve was created from…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - C.gigas GAPDH second rep on V.vulnificus exposure cDNA (from 20110311) and standard curves for COX1, COX2, GAPDH

2011

Miscellaneous

Jun 3, 2011

Ran a qPCR on all cDNA samples. Created a standard curve to possibly allow for use of the BioRad software for gene expression analysis. Standard curve was created from…

<<<<<<< HEAD

Jun 3, 2011

Ran a qPCR on all cDNA samples from the V.vulnificus exposure experiment from 20110111. This qPCR was to test 2 of 4 potential normalizing genes to evaluate which genes show…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - C.gigas actin and GAPDH on V.vulnificus exposure cDNA (from 20110311)

2011

Miscellaneous

Ran a qPCR on all cDNA samples from the V.vulnificus exposure experiment from 20110111. This qPCR was to test 2 of 4 potential normalizing genes to evaluate which genes show…

<<<<<<< HEAD

Ran a qPCR on all cDNA samples from the V.vulnificus exposure experiment from 20110111. This qPCR was to test 2 of 4 potential normalizing genes to evaluate which genes show…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - C.gigas 18s and EF1a on V.vulnificus exposure cDNA (from 20110311)

2011

Miscellaneous

Ran a qPCR on all cDNA samples from the V.vulnificus exposure experiment from 20110111. This qPCR was to test 2 of 4 potential normalizing genes to evaluate which genes show…

<<<<<<< HEAD

Ran a qPCR on all cDNA samples from the V.vulnificus exposure experiment from 20110111. Primers used were Cg_COX1/2_qPCR_F (SR ID: 1192) & Cg_COX2_454align1_R (SR ID: 1190).…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - C.gigas COX2 on V.vulnificus exposure cDNA (from 20110311)

2011

Miscellaneous

Ran a qPCR on all cDNA samples from the V.vulnificus exposure experiment from 20110111. Primers used were Cg_COX1/2_qPCR_F (SR ID: 1192) & Cg_COX2_454align1_R (SR ID: 1190).…

<<<<<<< HEAD

Ran a qPCR on all cDNA samples from the V.vulnificus exposure experiment from 20110111. Primers used were Cg_COX1/2_qPCR_F (SR ID: 1192) & Cg_COX1_qPCR_R (SR ID: 1191).…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - C.gigas COX1 on V.vulnificus exposure cDNA (from 20110311)

2011

Miscellaneous

Ran a qPCR on all cDNA samples from the V.vulnificus exposure experiment from 20110111. Primers used were Cg_COX1/2_qPCR_F (SR ID: 1192) & Cg_COX1_qPCR_R (SR ID: 1191).…

<<<<<<< HEAD

Ran a qPCR to evaluate a large batch of primers (40 sets) that were ordered per Steven, based off of the most recent SOLiD run (samples submitted 3/10/2011; see Dave’s…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Hard Clam NGS Primer Checks

2011

Miscellaneous

May 23, 2011

Ran a qPCR to evaluate a large batch of primers (40 sets) that were ordered per Steven, based off of the most recent SOLiD run (samples submitted 3/10/2011; see Dave’s…

<<<<<<< HEAD

May 23, 2011

Ran qPCR with Lexie’s cDNA samples from this experiment with the following primer sets in order to better evaluate her biological reps:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Lexie’s QPX Temp & Tissue Experiment (see Lexies Notebook 4/26/2011)

2011

Miscellaneous

Ran qPCR with Lexie’s cDNA samples from this experiment with the following primer sets in order to better evaluate her biological reps:

<<<<<<< HEAD

Due to previous contamination issues with Emma’s primers, Emma asked me to order new primers, reconstitute them and run a qPCR for her to see if we could eliminate her…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Emma’s New 3KDSqPCR Primers

2011

Miscellaneous

Due to previous contamination issues with Emma’s primers, Emma asked me to order new primers, reconstitute them and run a qPCR for her to see if we could eliminate her…

<<<<<<< HEAD

Performed reverse transcription on DNased RNA from the hard clam vibrio tubiashii challenge experiment (see Dave’s Notebook 5/2/2011), following the Promega M-MLV RT…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Reverse Transcription - Hard Clam Gill DNased RNA (from 20110509)

2011

Miscellaneous

May 11, 2011

Performed reverse transcription on DNased RNA from the hard clam vibrio tubiashii challenge experiment (see Dave’s Notebook 5/2/2011), following the Promega M-MLV RT…

<<<<<<< HEAD

May 11, 2011

DNased 5ug of RNA from each sample with Ambion’s Turbo DNA-free Kit, according to the manufacturer’s rigorous protocol. Samples were spec’d and stored @ -80C in the “Hard…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNase - Hard Clam Gill RNA (from earlier today)

2011

Miscellaneous

DNased 5ug of RNA from each sample with Ambion’s Turbo DNA-free Kit, according to the manufacturer’s rigorous protocol. Samples were spec’d and stored @ -80C in the “Hard…

<<<<<<< HEAD

Isolated RNA in 1mL of Tri-Reagent according to the manufacturer’s protocol. Also, finished RNA isolation of samples that were started 20110506. Samples were resuspended in…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation - Hard Clam Gill Tissue from Vibrio Experiment (see Dave’s Notebook 5/2/2011)

2011

Miscellaneous

Isolated RNA in 1mL of Tri-Reagent according to the manufacturer’s protocol. Also, finished RNA isolation of samples that were started 20110506. Samples were resuspended in…

<<<<<<< HEAD

Designed primers for 40 PCR targets derived from the most recent SOLiD data by Steven(Evernote link) using BatchPrimer3. BatchPrimer3 results are here.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Primer Design - Hard Clam NGS Primers

2011

Miscellaneous

Hard clam

Mercenaria mercenaria

primers

May 8, 2011

Designed primers for 40 PCR targets derived from the most recent SOLiD data by Steven(Evernote link) using BatchPrimer3. BatchPrimer3 results are here.

<<<<<<< HEAD

May 8, 2011

Isolated RNA in 1mL of Tri-Reagent according to manufacturer’s protocol. Samples were precipitated with isopropanol and stored over the weekend @ -20C. Will conclude…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation - Hard Clam Gill Tissue from Vibrio Experiment (see Dave’s Notebook 5/2/2011)

2011

Miscellaneous

May 6, 2011

Isolated RNA in 1mL of Tri-Reagent according to manufacturer’s protocol. Samples were precipitated with isopropanol and stored over the weekend @ -20C. Will conclude…

<<<<<<< HEAD

May 6, 2011

Received two bags containing ~24 live clams (didn’t count) in each bag. One bag labeled as “Mashpee Control” and the other “BX Selected.” Clams were stored @ 4C by Steven.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Received - Live Hard Clams From Scott Lindell

2011

Miscellaneous

Apr 28, 2011

Received two bags containing ~24 live clams (didn’t count) in each bag. One bag labeled as “Mashpee Control” and the other “BX Selected.” Clams were stored @ 4C by Steven.

<<<<<<< HEAD

Apr 28, 2011

Inoculated 5mL of 1x LB + Kan50 (made by Steven on 3/23/11). Incubated O/N at 37C, 250RPM. Will perform mini preps tomorrow. The following samples were selected:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Bacterial Cultures - Colonies Selected from Yesterday’s Colony PCRs

2011

Miscellaneous

Inoculated 5mL of 1x LB + Kan50 (made by Steven on 3/23/11). Incubated O/N at 37C, 250RPM. Will perform mini preps tomorrow. The following samples were selected:

<<<<<<< HEAD

Mini prepped 3mLs of each culture, according to Qiagen protocol. Samples were eluted with 50uL of Buffer EB.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Mini Preps - Liquid Cultures from yesterday

2011

Miscellaneous

Mini prepped 3mLs of each culture, according to Qiagen protocol. Samples were eluted with 50uL of Buffer EB.

<<<<<<< HEAD

Inoculated 5mL of 1x LB + Kan50 (made by Steven on 3/23/11). Incubated O/N @ 37C, 250RPM. Will perform mini preps tomorrow. The following samples were selected (red text on…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Bacterial Cultures - Colonies Selected by Steven from Steven’s Re-Streaked Plate

2011

Miscellaneous

Inoculated 5mL of 1x LB + Kan50 (made by Steven on 3/23/11). Incubated O/N @ 37C, 250RPM. Will perform mini preps tomorrow. The following samples were selected (red text on…

<<<<<<< HEAD

Ran colony PCR on various colonies produced from cloning on 20110411. All colonies were picked, re-streaked on Kan50 plate(s) and PCR’d. Master mix calcs are here. Cycling…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Colony PCR - Colonies from COX1 Genomic Cloning (from 20110411)

2011

Miscellaneous

Ran colony PCR on various colonies produced from cloning on 20110411. All colonies were picked, re-streaked on Kan50 plate(s) and PCR’d. Master mix calcs are here. Cycling…

<<<<<<< HEAD

Repeated yesterday’s PCR on the re-streaked colony in order to run the product on a gel with a more appropriate ladder. See yesterday’s entry for all PCR info.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Colony PCR - 5’RACE Colony: COX2 (repeat of yesterday’s PCR)

2011

Miscellaneous

Apr 22, 2011

Repeated yesterday’s PCR on the re-streaked colony in order to run the product on a gel with a more appropriate ladder. See yesterday’s entry for all PCR info.

<<<<<<< HEAD

Apr 22, 2011

One white colony (marked with arrow in image linked) from the two plates from Steven’s cloning (from yesterday) was picked, restreaked on a new Kan50 plate (no X-gal) and…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Colony PCR - 5’ RACE Colony: COX2

2011

Miscellaneous

Apr 21, 2011

One white colony (marked with arrow in image linked) from the two plates from Steven’s cloning (from yesterday) was picked, restreaked on a new Kan50 plate (no X-gal) and…

<<<<<<< HEAD

Apr 21, 2011

Two light blue colonies (there were no white colonies) were picked, restreaked on a new Kan50 plate (no X-gal) and PCR’d.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Colony PCR - 5’ RACE Colonies

2011

Miscellaneous

Apr 14, 2011

Two light blue colonies (there were no white colonies) were picked, restreaked on a new Kan50 plate (no X-gal) and PCR’d.

<<<<<<< HEAD

Apr 14, 2011

Performed ligations/cloning on a variety of COX1 genomic and COX 5’ RACE products using the TOPO TA Cloning Kit (Invitrogen). Used 2uL of gel-purified PCR product in each…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Ligations - COX1/COX2 PCR Products

2011

Miscellaneous

Apr 11, 2011

Performed ligations/cloning on a variety of COX1 genomic and COX 5’ RACE products using the TOPO TA Cloning Kit (Invitrogen). Used 2uL of gel-purified PCR product in each…

<<<<<<< HEAD

Apr 11, 2011

Due to the failure of the primary PCR on both 5’ and 3’ RACE cDNA libraries (from 20080619) yesterday, will perform nested PCR using a nested GSP designed by Steven…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

5’/3’ RACE PCRs - Nested PCRs for COX2 Sequence

2011

Miscellaneous

Apr 7, 2011

Due to the failure of the primary PCR on both 5’ and 3’ RACE cDNA libraries (from 20080619) yesterday, will perform nested PCR using a nested GSP designed by Steven…

<<<<<<< HEAD

Apr 7, 2011

Ran PCRs on both the 5’ & 3’ RACE libraries created 20080619 with a new COX2 gene-specifc (GSP) primer designed by Steven (CgPGSRACEsrGSP1; SR ID: 1208). Although this…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

5’/3’ RACE PCRs - COX2 Sequence on 5’ & 3’ RACE Libraries (from 20080619)

2011

Miscellaneous

Apr 6, 2011

Ran PCRs on both the 5’ & 3’ RACE libraries created 20080619 with a new COX2 gene-specifc (GSP) primer designed by Steven (CgPGSRACEsrGSP1; SR ID: 1208). Although this…

<<<<<<< HEAD

Apr 6, 2011

Performed qPCR using cDNA from 20110311. This was performed for 2 reps with TIMP3(BB) (SR IDs: 1067 & 1106). Master mix calcs are here. Plate layout, cycling params, etc.…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - C.gigas BB/DH cDNA for PROPS (TIMP3(BB) primers)

2011

PROPS

Performed qPCR using cDNA from 20110311. This was performed for 2 reps with TIMP3(BB) (SR IDs: 1067 & 1106). Master mix calcs are here. Plate layout, cycling params, etc.…

<<<<<<< HEAD

Performed qPCR using cDNA from 20110311. This was performed for 2 reps with HMGP (SR IDs:359 & 360). Master mix calcs are here. Plate layout, cycling params, etc can be…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - C.gigas BB/DH cDNA for PROPS (HMGP primers)

2011

PROPS

Performed qPCR using cDNA from 20110311. This was performed for 2 reps with HMGP (SR IDs:359 & 360). Master mix calcs are here. Plate layout, cycling params, etc can be…

<<<<<<< HEAD

Performed qPCR using pooled cDNA from 20110311. Pooled 2uL from each of the following samples groups: Dg 3hr C, Gill 1hr C, Gill 1hr E, Mantle 3hr C, and Muscle 3hr C. Master…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - C.gigas COX1/COX2 Tissue Distribution

2011

Miscellaneous

Mar 15, 2011

Performed qPCR using pooled cDNA from 20110311. Pooled 2uL from each of the following samples groups: Dg 3hr C, Gill 1hr C, Gill 1hr E, Mantle 3hr C, and Muscle 3hr C. Master…

<<<<<<< HEAD

Mar 15, 2011

Performed qPCR using cDNA from 20110311. This was performed for additional reps for TIMP3(BB) (SR IDs:1067 & 1106) and HMGP (SR IDs:359 & 360). Master mix calcs are here.…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - C.gigas BB/DH cDNA for PROPS

2011

PROPS

Mar 14, 2011

Performed qPCR using cDNA from 20110311. This was performed for additional reps for TIMP3(BB) (SR IDs:1067 & 1106) and HMGP (SR IDs:359 & 360). Master mix calcs are here.…

<<<<<<< HEAD

Mar 14, 2011

Performed RT on DNased RNA using Promega MMLV RT and Oligo dT according to manufacturer’s protocol, using 1ug of DNased RNA, but in a 50uL reaction. Due to large number of…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Reverse Transcription - C.gigas BB/DH DNased RNA (from 20090507) for PROPS

2011

PROPS

Performed RT on DNased RNA using Promega MMLV RT and Oligo dT according to manufacturer’s protocol, using 1ug of DNased RNA, but in a 50uL reaction. Due to large number of…

<<<<<<< HEAD

Performed RT on DNased RNA using Promega MMLV RT and Oligo dT according to manufacturer’s protocol, using 1ug of DNased RNA. Due to large number of samples, cDNA was made in…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Reverse Transcription - C.gigas DNased RNA (from 20110131) from V.vulnificus Exposure & Tissues (from 20110111)

2011

Miscellaneous

Performed RT on DNased RNA using Promega MMLV RT and Oligo dT according to manufacturer’s protocol, using 1ug of DNased RNA. Due to large number of samples, cDNA was made in…

<<<<<<< HEAD

Submitted the following 8 samples for SOLiD sequencing at HTGU:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

SOLiD Sequencing Submission

2011

Miscellaneous

Mar 10, 2011

Submitted the following 8 samples for SOLiD sequencing at HTGU:

<<<<<<< HEAD

Mar 10, 2011

mRNA was isolated for SOLiD sequencing by HTGU. Made two pools of San Nick RNA (Control and Exposed) using equal amounts (5ug) of each individual sample. Individual samples…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

mRNA Isolation - Pooled Black Abalone Dg RNA (from Abalone Dg Exp 1)

2011

Miscellaneous

Mar 7, 2011

mRNA was isolated for SOLiD sequencing by HTGU. Made two pools of San Nick RNA (Control and Exposed) using equal amounts (5ug) of each individual sample. Individual samples…

<<<<<<< HEAD

Mar 7, 2011

Used Cg_COX2_3’RACE_short (SR ID: 1197) & Cg_COX2_3’RACE_long (SR ID: 1196) and the Clonetech SMART RACE cDNA Amplification Kit (unknown acquisition date) to attempt to…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

3’RACE - C.gigas 3’RACE for COX2

2011

Miscellaneous

Mar 4, 2011

Used Cg_COX2_3’RACE_short (SR ID: 1197) & Cg_COX2_3’RACE_long (SR ID: 1196) and the Clonetech SMART RACE cDNA Amplification Kit (unknown acquisition date) to attempt to…

<<<<<<< HEAD

Mar 4, 2011

A previous comparison was performed (see 20110209), but it was determined that the standard DNA being used to test the machines was old/degraded. Lisa ordered a new standard…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

NanoDrop1000 Comparison - Roberts vs. Young Lab

2011

Miscellaneous

A previous comparison was performed (see 20110209), but it was determined that the standard DNA being used to test the machines was old/degraded. Lisa ordered a new standard…

<<<<<<< HEAD

Ran qPCR on DNased RNA from earlier today to verify removal of contaminating gDNA. Used C.gigas 18s primers (SR IDs: 156, 157). 0.5uL (~40ng) of DNased RNA was used for…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Check DNased RNA BB01 for Residual gDNA (from earlier today)

2011

PROPS

Ran qPCR on DNased RNA from earlier today to verify removal of contaminating gDNA. Used C.gigas 18s primers (SR IDs: 156, 157). 0.5uL (~40ng) of DNased RNA was used for…

<<<<<<< HEAD

Since the previous DNase treatment failed for this sample, will repeat but will start with less RNA (5ug instead of 10ug). Need more DNased RNA to finish repeating of PROPS.…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNase - C.gigas BB01 (PROPS) RNA (from 20090507)

2011

PROPS

Since the previous DNase treatment failed for this sample, will repeat but will start with less RNA (5ug instead of 10ug). Need more DNased RNA to finish repeating of PROPS.…

<<<<<<< HEAD

Ran qPCR on DNased RNA from earlier today to verify removal of contaminating gDNA. Used C.gigas 18s primers (SR IDs: 156, 157). 0.75uL (~50ng) of DNased RNA was used for…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Check DNased RNA BB01 for Residual gDNA (from earlier today)

2011

PROPS

Ran qPCR on DNased RNA from earlier today to verify removal of contaminating gDNA. Used C.gigas 18s primers (SR IDs: 156, 157). 0.75uL (~50ng) of DNased RNA was used for…

<<<<<<< HEAD

Used EtOH precipitated BB01 RNA from 20110225 and followed Ambion’s “rigorous” protocol, utilizing a total of 2uL of DNAse. Briefly, samples were incubated @ 37C for 30mins…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNase - C.gigas BB01 from 20110225

2011

PROPS

Used EtOH precipitated BB01 RNA from 20110225 and followed Ambion’s “rigorous” protocol, utilizing a total of 2uL of DNAse. Briefly, samples were incubated @ 37C for 30mins…

<<<<<<< HEAD

Due to residual gDNA contamination, will EtOH precipitate in order to treat with DNase again. Add 0.5 vols 3M NaAOc (pH=

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Ethanol Precpitation - DNased RNA BB01 (from earlier today)

2011

PROPS

Due to residual gDNA contamination, will EtOH precipitate in order to treat with DNase again. Add 0.5 vols 3M NaAOc (pH=

<<<<<<< HEAD

Ran qPCR on DNased RNA from earlier today to verify removal of contaminating gDNA. Used C.gigas 18s primers (SR IDs: 156, 157). 0.5uL (50ng) of DNased RNA was used for…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Check DNased RNA BB01 for Residual gDNA (from earlier today)

2011

PROPS

Ran qPCR on DNased RNA from earlier today to verify removal of contaminating gDNA. Used C.gigas 18s primers (SR IDs: 156, 157). 0.5uL (50ng) of DNased RNA was used for…

<<<<<<< HEAD

Used EtOH precipitated BB01 RNA from 20110216 and followed Ambion’s “rigorous” protocol, utilizing a total of 2uL of DNAse. Briefly, samples were incubated @ 37C for 30mins…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNase - C.gigas BB01 from 20110216

2011

PROPS

Used EtOH precipitated BB01 RNA from 20110216 and followed Ambion’s “rigorous” protocol, utilizing a total of 2uL of DNAse. Briefly, samples were incubated @ 37C for 30mins…

<<<<<<< HEAD

Due to residual gDNA contamination, will EtOH precipitate in order to treat with DNase again. Add 0.5 vols 3M NaAOc (pH = 5.2), 2.5 vols 100% EtOH, mixed and incubated @…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Ethanol Precipitation - DNased RNA BB01 (from earlier today)

2011

PROPS

Due to residual gDNA contamination, will EtOH precipitate in order to treat with DNase again. Add 0.5 vols 3M NaAOc (pH = 5.2), 2.5 vols 100% EtOH, mixed and incubated @…

<<<<<<< HEAD

Ran qPCR on DNased RNA from earlier today to verify that it was free of contaminating gDNA. Used C.gigas 18s primers (SR IDs: 156, 157). 0.5uL (50ng) of DNased RNA was used…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Check DNased RNA BB01 & 09 (from earlier today)

2011

PROPS

Ran qPCR on DNased RNA from earlier today to verify that it was free of contaminating gDNA. Used C.gigas 18s primers (SR IDs: 156, 157). 0.5uL (50ng) of DNased RNA was used…

<<<<<<< HEAD

Need more DNased RNA to finish repeating of PROPS. Some samples had insufficient quantities of DNased RNA remaining in BB01 and BB09. Used 10ug of each RNA and followed…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNase - C.gigas BB/DH (PROPS) RNA (from 20090507)

2011

PROPS

Need more DNased RNA to finish repeating of PROPS. Some samples had insufficient quantities of DNased RNA remaining in BB01 and BB09. Used 10ug of each RNA and followed…

<<<<<<< HEAD

All runs (3 runs were conducted) were created using a master mix containing C.gigas gDNA (either 50ng or 100ng), 1X Promega qPCR Master Mix, 0.2uM each of forward/reverse…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Data Analysis - Young Lab ABI 7300 Calibration Checks

2011

Miscellaneous

All runs (3 runs were conducted) were created using a master mix containing C.gigas gDNA (either 50ng or 100ng), 1X Promega qPCR Master Mix, 0.2uM each of forward/reverse…

<<<<<<< HEAD

This is a repeat of the two runs from yesterday, just to see if there is a correlation between the failed plates being the first of the day or not. Master mix calcs and…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Test Young Lab qPCR Calibration

2011

Miscellaneous

This is a repeat of the two runs from yesterday, just to see if there is a correlation between the failed plates being the first of the day or not. Master mix calcs and…

<<<<<<< HEAD

Due to an apparent reduction in assay sensitivity for the Hematodidium qPCR assay, we have decided to determine if the spec readings of the plasmid DNA being used for the…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

NanoDrop1000 Comparison - Roberts vs. Young Lab

2011

Miscellaneous

Due to an apparent reduction in assay sensitivity for the Hematodidium qPCR assay, we have decided to determine if the spec readings of the plasmid DNA being used for the…

<<<<<<< HEAD

This was repeated from earlier today due to the failure of the previous run, but had to use new gDNA since I ran out of the stock I had previously used. Master mix calcs and…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Test Young Lab qPCR Calibration (Repeat)

2011

Miscellaneous

This was repeated from earlier today due to the failure of the previous run, but had to use new gDNA since I ran out of the stock I had previously used. Master mix calcs and…

<<<<<<< HEAD

Used new primers for obtaining bands for additional sequencing of both COX isoforms in C. gigas. Master mix calcs are here. Master mix shorthand (MM##) is described below:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

PCR - New C. gigas COX Primers for Sequencing of Isoforms

2011

Miscellaneous

Used new primers for obtaining bands for additional sequencing of both COX isoforms in C. gigas. Master mix calcs are here. Master mix shorthand (MM##) is described below:

<<<<<<< HEAD

This is a repeat of a run from 20110204. Here’re master mix calcs. This was being repeated to evaluate whether or not the relative differences in Ct values observed on…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Test Young Lab qPCR Calibration (Repeat)

2011

Miscellaneous

This is a repeat of a run from 20110204. Here’re master mix calcs. This was being repeated to evaluate whether or not the relative differences in Ct values observed on…

<<<<<<< HEAD

This is a repeat of an earlier run from today, but with a different qPCR plate. [Here’re master mix calcs (bottom half of…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Test Young Lab qPCR Calibration (Repeat)

2011

Miscellaneous

This is a repeat of an earlier run from today, but with a different qPCR plate. [Here’re master mix calcs (bottom half of…

<<<<<<< HEAD

Recently, the Young Lab’s ABI 7300 qPCR machine was calibrated. Steven asked me to run a plate and see how well the calibration worked. Ran a plate with C.gigas gDNA and…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Test Young Lab qPCR Calibration

2011

Miscellaneous

Recently, the Young Lab’s ABI 7300 qPCR machine was calibrated. Steven asked me to run a plate and see how well the calibration worked. Ran a plate with C.gigas gDNA and…

<<<<<<< HEAD

This was repeated to generate more PCR product for sequencing purposes. PCR master mix calcs and cycling params are here. Master mixes 04 and 05 (MM04 and MM05) were…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genomic PCR - Repeat of C.gigas COX genomic PCR from 20110118

2011

Miscellaneous

Jan 31, 2011

This was repeated to generate more PCR product for sequencing purposes. PCR master mix calcs and cycling params are here. Master mixes 04 and 05 (MM04 and MM05) were…

<<<<<<< HEAD

Jan 31, 2011

5ug of RNA was DNased using Ambion’s Turbo DNA-free kit, following the rigorous protocol (0.5uL of DNase for 30 mins then additional 0.5uL of DNase for 30mins). Calcs for…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNase - DNase C.gigas RNA from 20110120, 20110121 and 20110124

2011

Miscellaneous

Jan 28, 2011

5ug of RNA was DNased using Ambion’s Turbo DNA-free kit, following the rigorous protocol (0.5uL of DNase for 30 mins then additional 0.5uL of DNase for 30mins). Calcs for…

<<<<<<< HEAD

Jan 28, 2011

RNA was isolated in 1mL TriReagent, according to protocol. Samples were resuspended in 50uL 0.1% DEPC-H2O and spec’d. RNA was stored @ -80C in “Shellfish RNA Box #4

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation - Various C.gigas Tissue from 20110111

2011

Miscellaneous

Jan 24, 2011

RNA was isolated in 1mL TriReagent, according to protocol. Samples were resuspended in 50uL 0.1% DEPC-H2O and spec’d. RNA was stored @ -80C in “Shellfish RNA Box #4

<<<<<<< HEAD

Jan 24, 2011

RNA was isolated in 1mL TriReagent, according to protocol. Samples were resuspended in 50uL 0.1% DEPC-H2O and spec’d. RNA was stored @ -80C in “Shellfish RNA Box #4”.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation - Various C.gigas Tissue from 20110111

2011

Miscellaneous

Jan 21, 2011

RNA was isolated in 1mL TriReagent, according to protocol. Samples were resuspended in 50uL 0.1% DEPC-H2O and spec’d. RNA was stored @ -80C in “Shellfish RNA Box #4”.

<<<<<<< HEAD

Jan 21, 2011

RNA was isolated in 1mL TriReagent, according to protocol. Samples were resuspended in 50uL 0.1% DEPC-H2O and spec’d. RNA was stored @ -80C in “Shellfish RNA Box #4”.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation - Various C.gigas Tissue from 20110111

2011

Miscellaneous

Jan 20, 2011

RNA was isolated in 1mL TriReagent, according to protocol. Samples were resuspended in 50uL 0.1% DEPC-H2O and spec’d. RNA was stored @ -80C in “Shellfish RNA Box #4”.

<<<<<<< HEAD

Jan 20, 2011

Attempt to obtain full genomic sequence for C.gigas COX. PCR set up/cycling params/etc are here. Primer set combinations(master mixes) are as follows:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Genomic PCR - C.gigas cyclooxygenase (COX) genomic sequence

2011

Miscellaneous

Jan 18, 2011

Attempt to obtain full genomic sequence for C.gigas COX. PCR set up/cycling params/etc are here. Primer set combinations(master mixes) are as follows:

<<<<<<< HEAD

Jan 18, 2011

All dilutions were performed with 1x LB+ 1%NaCl. 100uL were plated of all dilutions (see below) on 1xLB+1%NaCL plates. Plates were incubated O/N @ 37C. Colonies will be…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Bacterial Dilutions - Determination of Colony Forming Units from Gigas Bacterial challenge (from earlier today)

2011

Miscellaneous

All dilutions were performed with 1x LB+ 1%NaCl. 100uL were plated of all dilutions (see below) on 1xLB+1%NaCL plates. Plates were incubated O/N @ 37C. Colonies will be…

<<<<<<< HEAD

400mL O/N culture (1x LB+1% NaCl, 37C, 150RPM, 1L flask) of V.vulnificus (STRAIN??) and V.tubiashii (Strain: RE22) were pelleted (4300RPM, 25C, Sorvall ST-H750 rotor). Supe…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Gigas Bacterial Challenge - 1hr & 3hr Challenges with Vibrio vulnificus

2011

Miscellaneous

400mL O/N culture (1x LB+1% NaCl, 37C, 150RPM, 1L flask) of V.vulnificus (STRAIN??) and V.tubiashii (Strain: RE22) were pelleted (4300RPM, 25C, Sorvall ST-H750 rotor). Supe…

<<<<<<< HEAD

Retrieved the following SOLiD libraries from the CEG and stored in -80C in the “NGS Libraries” Box.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

SOLiD - Retrieved SOLiD Library Samples from CEG from 20101213

2010

Miscellaneous

Dec 23, 2010

Retrieved the following SOLiD libraries from the CEG and stored in -80C in the “NGS Libraries” Box.

<<<<<<< HEAD

Dec 23, 2010

Used COX primers (SR IDs 1060, 1061) and cDNA from 20080327, which consisted of 7 control gigas gill and 7 vibrio-exposed (24hrs) gigas gill samples, labeled as C# and VE#…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - COX qPCR Vibrio Exposure Response Check

2010

Miscellaneous

Dec 13, 2010

Used COX primers (SR IDs 1060, 1061) and cDNA from 20080327, which consisted of 7 control gigas gill and 7 vibrio-exposed (24hrs) gigas gill samples, labeled as C# and VE#…

<<<<<<< HEAD

Dec 13, 2010

Used new cyclooxygenase primers (SR IDs 1060, 1061) to see how they performed and to evaluate tissue distribution. Tissue distribution was evaluated using the following…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - COX qPCR Primer Test and Tissue Distribution

2010

Miscellaneous

Dec 10, 2010

Used new cyclooxygenase primers (SR IDs 1060, 1061) to see how they performed and to evaluate tissue distribution. Tissue distribution was evaluated using the following…

<<<<<<< HEAD

Dec 10, 2010

Reaction calculations are here. Samples were mixed and incubated @ 37C O/N (started at 6PM). Mac will take care of them tomorrow morning.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Restriction Digestions/Ligations - MS-AFLP

2010

Miscellaneous

Nov 30, 2010

Reaction calculations are here. Samples were mixed and incubated @ 37C O/N (started at 6PM). Mac will take care of them tomorrow morning.

<<<<<<< HEAD

Nov 30, 2010

1st of 2 rounds of digests were performed. Calculations are here. Samples were incubated 37C for 3hrs, heat inactivated @ 80C for 30mins and then stored @ -20C.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Restriction Digestions - HpaII and MspI on Mac’s C.gigas Samples: Round 1

2010

Miscellaneous

1st of 2 rounds of digests were performed. Calculations are here. Samples were incubated 37C for 3hrs, heat inactivated @ 80C for 30mins and then stored @ -20C.

<<<<<<< HEAD

Samples were EtOH precipitated, according to protocol. Samples were resuspended in 20uL of Qiagen’s EB and spec’d.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

EtOH Precipitations - HpaII and MspI 2nd Round Digests from 20101124

2010

Miscellaneous

Samples were EtOH precipitated, according to protocol. Samples were resuspended in 20uL of Qiagen’s EB and spec’d.

<<<<<<< HEAD

Continued with 2nd round of digestions from yesterday. All samples were resuspended in 25uL of H2O yesterday, so brought volume up to 44uL with H2O, added 5uL of appropriate…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Restriction Digestions - HpaII and MspI on Mac’s C.gigas Samples: Round 2

2010

Miscellaneous

Nov 24, 2010

Continued with 2nd round of digestions from yesterday. All samples were resuspended in 25uL of H2O yesterday, so brought volume up to 44uL with H2O, added 5uL of appropriate…

<<<<<<< HEAD

Nov 24, 2010

Restriction digests from yesterday were mixed with equal volume (50uL) of phenol:chloroform:IAA (25:24:1) and centrifuged 16,000g for 5mins @ 4C. Aqueous phase was…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Phenol:Chloroform Extractions and EtOH Precipitations - HapII and MspI digests from yesterday

2010

Miscellaneous

Nov 23, 2010

Restriction digests from yesterday were mixed with equal volume (50uL) of phenol:chloroform:IAA (25:24:1) and centrifuged 16,000g for 5mins @ 4C. Aqueous phase was…

<<<<<<< HEAD

Nov 23, 2010

Set up restriction digests for subsequent analysis by methylation specific PCR (MSP). This will be the first of two rounds of digestion with the same enzyme on each sample. S…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Restriction Digestions - HpaII and MspI on Mac’s C.gigas gDNA Samples: Round 1

2010

Miscellaneous

Nov 22, 2010

Set up restriction digests for subsequent analysis by methylation specific PCR (MSP). This will be the first of two rounds of digestion with the same enzyme on each sample. S…

<<<<<<< HEAD

Nov 22, 2010

Washed 4 day old QPX cultures. 3 isolates (S-1, TD-81, ATCC), two flasks (13mL) of each were washed in the following manner:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

QPX Washes

2010

Miscellaneous

Washed 4 day old QPX cultures. 3 isolates (S-1, TD-81, ATCC), two flasks (13mL) of each were washed in the following manner:

<<<<<<< HEAD

Isolated gDNA from gray whale skin, human cheek cells (my own!) and two different species of algae (species 1, species 2) using Qiagen’s DNEasy Blood & Tissue Kit according…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

gDNA Isolation

2010

Miscellaneous

Isolated gDNA from gray whale skin, human cheek cells (my own!) and two different species of algae (species 1, species 2) using Qiagen’s DNEasy Blood & Tissue Kit according…

<<<<<<< HEAD

Precipitated whale gDNA in hopes of producing a sample with a higher concentration. Added 0.1 vols of 3M NaOAc (10uL), 2.5 vols of 100% EtOH (275uL), mixed thoroughly and…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

EtOH Precipitation - Whale gDNA from 20101022

2010

Miscellaneous

Oct 25, 2010

Precipitated whale gDNA in hopes of producing a sample with a higher concentration. Added 0.1 vols of 3M NaOAc (10uL), 2.5 vols of 100% EtOH (275uL), mixed thoroughly and…

<<<<<<< HEAD

Oct 25, 2010

Isolated gDNA from crab (unknown species), starfish exposed to RoundUp (unknown species) and gray whale blubber using Qiagen’s DNEasy Kit, according to manufacturer’s…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

gDNA Isolation

2010

Miscellaneous

Oct 22, 2010

Isolated gDNA from crab (unknown species), starfish exposed to RoundUp (unknown species) and gray whale blubber using Qiagen’s DNEasy Kit, according to manufacturer’s…

<<<<<<< HEAD

Oct 22, 2010

Received 82 gill samples in RNA Later in 3 microfuge tube racks from MBL (Scott Lindell). Samples were catalogued, boxed (1 box) and stored at -80C.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Received Hard Clam Samples and Live Clams from MBL

2010

Miscellaneous

Oct 19, 2010

Received 82 gill samples in RNA Later in 3 microfuge tube racks from MBL (Scott Lindell). Samples were catalogued, boxed (1 box) and stored at -80C.

<<<<<<< HEAD

Oct 19, 2010

30 gill tissue samples in RNA Later from CA, MA, & MAX each.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Received Hard Clam Samples from Rutgers

2010

Miscellaneous

Oct 15, 2010

30 gill tissue samples in RNA Later from CA, MA, & MAX each.

<<<<<<< HEAD

Oct 15, 2010

Ran a full plate for testing well-to-well consistency (or, inconsistency!) of the Opticon 2, since it’s been behaving poorly lately. This will provide us with an idea of…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Test Plate for Opticon 2

2010

Miscellaneous

Oct 12, 2010

Ran a full plate for testing well-to-well consistency (or, inconsistency!) of the Opticon 2, since it’s been behaving poorly lately. This will provide us with an idea of…

<<<<<<< HEAD

Oct 12, 2010

Distributed 50uL of FAM calibration dye to wells. Ran out of dye!!

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Opticon Calibration

2010

Miscellaneous

Sep 17, 2010

Distributed 50uL of FAM calibration dye to wells. Ran out of dye!!

<<<<<<< HEAD

Sep 17, 2010

Performed qPCR on Friedman Lab machine targeting immune-related genes in hard clam. Rough plate layout/master mix calcs are here. qPCR report from Friedman Lab machine is here…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Hard Clam Primers on cDNA from yesterday

2010

Miscellaneous

BigDef

C1qTNG

CFX96

CytP450-like

ferritnin

graphs

GST

Hard clam

HemoDef

HSP 70

Immomix

lysozyme

MAX

Mercenaria mercenaria

Mercenaria_Rel

metallothionein

Mm_TRAF6

NADHIV

qPCR

RACK1

SenescentProt

STI

SYTO 13

TfAP1

TLR

Sep 9, 2010

Performed qPCR on Friedman Lab machine targeting immune-related genes in hard clam. Rough plate layout/master mix calcs are here. qPCR report from Friedman Lab machine is here…

<<<<<<< HEAD

Sep 9, 2010

Prepared cDNA using 1ug of RNA from each of the 3 pools (CA, MA, MAX) and processed according to Promega’s M-MLV protocol, using oligo dT primers. Calcs and master mix set…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Reverse Transcription - DNased Hard Clam RNA from earlier today

2010

Miscellaneous

Prepared cDNA using 1ug of RNA from each of the 3 pools (CA, MA, MAX) and processed according to Promega’s M-MLV protocol, using oligo dT primers. Calcs and master mix set…

<<<<<<< HEAD

Pooled 2ug of each sample in each group (MAX, CA, MA) for a total of 6ug of RNA (3 total samples), brought volume up to 50uL and DNased using Ambion’s Turbo DNA-free…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNase - DNasing Hard Clam RNA from yesterday

2010

Miscellaneous

Pooled 2ug of each sample in each group (MAX, CA, MA) for a total of 6ug of RNA (3 total samples), brought volume up to 50uL and DNased using Ambion’s Turbo DNA-free…

<<<<<<< HEAD

RNA was mixed with 0.1 vols of 3M NAOAc (pH = 5.2) and 2.5 vols of 100% EtOH, vortexed and incubated @ -20C for 30mins. RNA was pelleted @ 16,000g, 30mins, 4C. Supe was…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

EtOH Precipitation - Hard Clam RNA from earlier today

2010

Miscellaneous

RNA was mixed with 0.1 vols of 3M NAOAc (pH = 5.2) and 2.5 vols of 100% EtOH, vortexed and incubated @ -20C for 30mins. RNA was pelleted @ 16,000g, 30mins, 4C. Supe was…

<<<<<<< HEAD

RNA was isolated from the following samples using TriReagent, according to protocol:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation - Hard Clam Tissues Rec’d from Rutgers on 20100820

2010

Miscellaneous

RNA was isolated from the following samples using TriReagent, according to protocol:

<<<<<<< HEAD

Rec’d package from Scott Lindell @ MBL containing 65 screw cap tubes in a white microtube rack. All tubes are tissues in RNA Later (presumably). One sample (MA4-5) was lost…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Package - Hard Clam Samples from MBL

2010

Miscellaneous

Sep 2, 2010

Rec’d package from Scott Lindell @ MBL containing 65 screw cap tubes in a white microtube rack. All tubes are tissues in RNA Later (presumably). One sample (MA4-5) was lost…

<<<<<<< HEAD

Sep 2, 2010

Rec’d package of hard clam samples from Emily @ Rutgers on wet ice. Package contained numerous 1.5mL snap cap tubes separated in to groups in zip lock bags. Stored…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Package - Hard Clam Samples from Rutgers

2010

Miscellaneous

Aug 20, 2010

Rec’d package of hard clam samples from Emily @ Rutgers on wet ice. Package contained numerous 1.5mL snap cap tubes separated in to groups in zip lock bags. Stored…

<<<<<<< HEAD

Aug 20, 2010

qPCR plate layout/setup is here.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - HpaII/MspI Digests from earlier today

2010

Miscellaneous

qPCR plate layout/setup is here.

<<<<<<< HEAD

Digest master mixes are here. Digests were incubated @ 37C for 2hrs. and then heat inactivated @ 80C for 20mins.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Restriction Digests - Various gigas gDNA from earlier today

2010

Miscellaneous

Digest master mixes are here. Digests were incubated @ 37C for 2hrs. and then heat inactivated @ 80C for 20mins.

<<<<<<< HEAD

Pelleted residual tissue 10mins @ 10,000g @ RT. Transferred supe to new tubes. Precipitated DNA with 0.25mL 100% EtOH. Incubated 3mins @ RT. DNA was pelleted 5mins @ 5000g @…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

gDNA Isolation - Various gigas samples (continued from yesterday)

2010

Miscellaneous

Pelleted residual tissue 10mins @ 10,000g @ RT. Transferred supe to new tubes. Precipitated DNA with 0.25mL 100% EtOH. Incubated 3mins @ RT. DNA was pelleted 5mins @ 5000g @…

<<<<<<< HEAD

Placed ~20mg fragments of tissue in 250uL DNAzol. Added 1.35uL of Proteinase K (Fermentas; 18.5mg/mL) to reach a final concentration of 100ug/mL. Incubated RT, O/N…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

gDNA Isolation - Various gigas samples

2010

Miscellaneous

Placed ~20mg fragments of tissue in 250uL DNAzol. Added 1.35uL of Proteinase K (Fermentas; 18.5mg/mL) to reach a final concentration of 100ug/mL. Incubated RT, O/N…

<<<<<<< HEAD

Finished EtOH precipitation of MeDIP gDNA. Samples were pelleted 16,000g, 4C, 30mins. Supe was discarded. Washed with 1mL 70% EtOH, pelleted 16,000g, 4C, 15mins. Supe…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

MeDIP - SB/WB Fragmented gDNA EtOH precipitation (continued from 20100702)

2010

Miscellaneous

Finished EtOH precipitation of MeDIP gDNA. Samples were pelleted 16,000g, 4C, 30mins. Supe was discarded. Washed with 1mL 70% EtOH, pelleted 16,000g, 4C, 15mins. Supe…

<<<<<<< HEAD

Continued MeDIP process from yesterday. Protein A/G beads were pelleted XXXXXXXXX, supe transferred to clean tube. Beads were washed 3x in the following fashion, each wash…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

MeDIP - SB/WB Fragmented gDNA (continued from yesterday)

2010

Miscellaneous

Continued MeDIP process from yesterday. Protein A/G beads were pelleted XXXXXXXXX, supe transferred to clean tube. Beads were washed 3x in the following fashion, each wash…

<<<<<<< HEAD

Performed restriction digests. Made dilutions of all DNAs involved of 25ng/uL. Made enough for a total of 9 digests could be performed on each DNA. This allowed using 10uL…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Restriction Digests - Various gigas gDNAs of Mac’s

2010

Miscellaneous

Performed restriction digests. Made dilutions of all DNAs involved of 25ng/uL. Made enough for a total of 9 digests could be performed on each DNA. This allowed using 10uL…

<<<<<<< HEAD

Continued MeDIP process from yesterday. Added 20uL of Protein A/G Plus Agarose (Santa Cruz Biotech) beads to each sample and continued incubation with rotation @ 4C for…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

MeDIP - SB/WB Fragmented gDNA (continued from yesterday)

2010

Miscellaneous

Jul 1, 2010

Continued MeDIP process from yesterday. Added 20uL of Protein A/G Plus Agarose (Santa Cruz Biotech) beads to each sample and continued incubation with rotation @ 4C for…

<<<<<<< HEAD

Jul 1, 2010

After confirming proper fragmentation (~460bp average fragment size) via Bioanalyzer earlier today, began the MeDIP process. Brought fragmented DNA samples up to 350uL with…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

MeDIP - SB/WB Fragmented gDNA (from 20100625)

2010

Miscellaneous

After confirming proper fragmentation (~460bp average fragment size) via Bioanalyzer earlier today, began the MeDIP process. Brought fragmented DNA samples up to 350uL with…

<<<<<<< HEAD

To gain a more quantitative assessment of the fragmentation from 20100625, I ran 1uL of each sample (~55ng, according to pre-fragmentation spec values) on the Agilent…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Bioanalyzer - Fragmented SB/WB gDNA (from 20100625)

2010

Miscellaneous

To gain a more quantitative assessment of the fragmentation from 20100625, I ran 1uL of each sample (~55ng, according to pre-fragmentation spec values) on the Agilent…

<<<<<<< HEAD

The previous attempt at sonication (see 20100618) failed, likely due to no using the correct equipment (tubes and Covaris adapter). The two gDNA pools, which had previously…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

gDNA Sonication - SB/WB gDNA pools (prep for MeDIP) from 20100618

2010

Miscellaneous

Jun 25, 2010

The previous attempt at sonication (see 20100618) failed, likely due to no using the correct equipment (tubes and Covaris adapter). The two gDNA pools, which had previously…

<<<<<<< HEAD

Jun 25, 2010

Received sets of gill tissue and hemolymph in RNA Later from Rutgers (Emily). Here’s the note that was included with the samples.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Samples Received - Hard Clam samples from Rutgers and MBL

2010

Miscellaneous

Jun 24, 2010

Received sets of gill tissue and hemolymph in RNA Later from Rutgers (Emily). Here’s the note that was included with the samples.

<<<<<<< HEAD

Jun 24, 2010

The two gDNA pools (SB and WB) were sonicated using a Covaris S2. Used the guidelines of the manufacturer (listed below) for shearing gDNA to a desired target size (500bp):

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

gDNA Sonication - SB/WB gDNA pools (prep for MeDIP) from earlier today

2010

Miscellaneous

The two gDNA pools (SB and WB) were sonicated using a Covaris S2. Used the guidelines of the manufacturer (listed below) for shearing gDNA to a desired target size (500bp):

<<<<<<< HEAD

8 gDNA samples from SB were pooled and 8 gDNA samples from WB were pooled, using equal amounts of gDNA from each sample (1250ng) for a total of 10ug (see SB/WB Mac’s MeDIP…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

gDNA Precipitation - SB/WB gDNA pools (prep for MeDIP)

2010

Miscellaneous

8 gDNA samples from SB were pooled and 8 gDNA samples from WB were pooled, using equal amounts of gDNA from each sample (1250ng) for a total of 10ug (see SB/WB Mac’s MeDIP…

<<<<<<< HEAD

Continued gDNA isolation of the above mentioned larvae samples that was started by Mac yesterday. Amount of larvae in tubes looked disproportionately large, relative to the…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

gDNA Isolation - Mac gigas larvae samples: control larvae 6.7.10 and 5-aza tr larvae 6.7.10

2010

Miscellaneous

5-azacitidine

Crassostrea gigas

DNA Isolation

DNA Quantification

DNazol

gDNA

larvae

NanoDrop1000

Pacific oyster

Jun 8, 2010

Continued gDNA isolation of the above mentioned larvae samples that was started by Mac yesterday. Amount of larvae in tubes looked disproportionately large, relative to the…

<<<<<<< HEAD

Jun 8, 2010

Continued with gDNA isolation from yesterday’s samples. Samples were gently pipetted up and down to further dissolve remaining tissue, although tissue did not dissolve…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

gDNA Isolation - Mac gigas gill samples (continued from yesterday)

2010

Miscellaneous

Crassostrea gigas

DNA Isolation

DNA Quantification

DNazol

gDNA

gel

gill

NanoDrop1000

Pacific oyster

R37

R51

RNAlater

Jun 5, 2010

Continued with gDNA isolation from yesterday’s samples. Samples were gently pipetted up and down to further dissolve remaining tissue, although tissue did not dissolve…

<<<<<<< HEAD

Jun 5, 2010

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

gDNA Isolation - Mac gigas gill samples

2010

Miscellaneous

Crassostrea gigas

DNA Isolation

DNazol

gill

Pacific oyster

R37

R51

RNAlater

Jun 4, 2010

<<<<<<< HEAD

Jun 4, 2010

Continued with gDNA isolation from yesterday’s samples. Additionally, isolated gDNA from R51 01, but homogenized the tissue (using disposable 1.5mL mortar/pestle) in 0.5mL…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

gDNA Isolation - Mac gigas gill samples (continued from yesterday)

2010

Miscellaneous

May 28, 2010

Continued with gDNA isolation from yesterday’s samples. Additionally, isolated gDNA from R51 01, but homogenized the tissue (using disposable 1.5mL mortar/pestle) in 0.5mL…

<<<<<<< HEAD

May 28, 2010

Rec’d 6 15mL conical tubes with liquid cultures of various algae. It appears that we rec’d two of each culture. No note/info included with package. Tubes will be stored @ RT…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Package Rec’d - From NOAA in Connecticut

2010

Miscellaneous

algae

Isochrysis sp. T-150

NOAA

package

Tetraselmis cheri Ply429

Thalassiaosira weissflugii TW

Rec’d 6 15mL conical tubes with liquid cultures of various algae. It appears that we rec’d two of each culture. No note/info included with package. Tubes will be stored @ RT…

<<<<<<< HEAD

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

gDNA Isolation - Mac gigas gill samples

2010

Miscellaneous

Crassostrea gigas

DNazol

Pacific oyster

R51

RNAlater

<<<<<<< HEAD

ePCR was performed following ABI’s “full scale” protocol, using 1pM of SOLiD cDNA library.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

SOLiD ePCR/Templated Bead Prep - Lake Trout Lean library

2010

Miscellaneous

May 26, 2010

ePCR was performed following ABI’s “full scale” protocol, using 1pM of SOLiD cDNA library.

<<<<<<< HEAD

May 26, 2010

Templated bead preparation was performed according to the “full scale” protocol.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

SOLiD Templated Bead Prep - Yellow perch CT, WB and lake trout Lean libraries (continued from yesterday)

2010

Miscellaneous

May 13, 2010

Templated bead preparation was performed according to the “full scale” protocol.

<<<<<<< HEAD

May 13, 2010

Performed ePCRs on these samples from DATE, following the “full scale” protocol. A work flow analysis (WFA) run on these samples from the initial ePCRs/templated bead prep…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

SOLiD ePCRs - Yellow perch CT, WB and lake trout Lean libraries

2010

Miscellaneous

May 12, 2010

Performed ePCRs on these samples from DATE, following the “full scale” protocol. A work flow analysis (WFA) run on these samples from the initial ePCRs/templated bead prep…

<<<<<<< HEAD

May 12, 2010

Rec’d package from Rutgers (Emily Pearson) containing two large Ziplock bags on “wet” ice, each of those containing smaller bags with sample tubes in them. One large bag…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Package - Hard Clam gill tissue/hemolymph in RNA later

2010

Miscellaneous

Rec’d package from Rutgers (Emily Pearson) containing two large Ziplock bags on “wet” ice, each of those containing smaller bags with sample tubes in them. One large bag…

<<<<<<< HEAD

Note: This information was added 20140407. Yes, you read that correctly.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Isolation - Qiagen Kit Comparison

2010

Miscellaneous

DNeasy

gDNA

gel

Hyperladder I

troubleshooting

Note: This information was added 20140407. Yes, you read that correctly.

<<<<<<< HEAD

Utilized to sets of primers obtained from the Friedman Lab: VptA (referred to as “Hasegawa”, even though the reference article calls the primers Vtp A) and Vt IGS (referred…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - V.tubiashii primers test (Vpt A and Vt IGS)

2010

Miscellaneous

May 3, 2010

Utilized to sets of primers obtained from the Friedman Lab: VptA (referred to as “Hasegawa”, even though the reference article calls the primers Vtp A) and Vt IGS (referred…

<<<<<<< HEAD

May 3, 2010

All libraries were prepped according to ABI’s “full-scale” bead prep protocol. Initial bead counts were performed using a hemocytometer in a 1:200 dilution:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Templated Bead Prep SOLiD Libraries - Yellow perch WB, lake trout Lean and Sisco, and herring G/O HWS09 libraries

2010

Miscellaneous

Apr 16, 2010

All libraries were prepped according to ABI’s “full-scale” bead prep protocol. Initial bead counts were performed using a hemocytometer in a 1:200 dilution:

<<<<<<< HEAD

Apr 16, 2010

ePCR was performed for the above three mentioned SOLiD libraries using 1.5pM (180 pg/uL) of cDNA, according to the ABI “full scale” ePCR protocol. ePCRs were stored @ 4C…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

ePCR SOLiD Libraries - Lake Trout Sisco and Herring G/O HPWS09 libraries (from 20100408)

2010

Miscellaneous

Apr 15, 2010

ePCR was performed for the above three mentioned SOLiD libraries using 1.5pM (180 pg/uL) of cDNA, according to the ABI “full scale” ePCR protocol. ePCRs were stored @ 4C…

<<<<<<< HEAD

Apr 15, 2010

All libraries were prepped according to ABI’s “full-scale” bead prep protocol. Initial bead counts were performed using a hemocytometer in a 1:200 dilution:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Templated Bead Prep SOLiD Libraries - Abalone CC, CE pools and yellow perch CT, PQ libraries

2010

Miscellaneous

Apr 14, 2010

All libraries were prepped according to ABI’s “full-scale” bead prep protocol. Initial bead counts were performed using a hemocytometer in a 1:200 dilution:

<<<<<<< HEAD

Apr 14, 2010

ePCR was performed for the above three mentioned SOLiD libraries using 1.5pM (180 pg/uL) of cDNA, according to the ABI “full scale” ePCR protocol. ePCRs were stored @ 4C…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

ePCR SOLiD Libraries - Yellow perch PQ, WB and Lake Trout Lean libraries (from 20100408)

2010

Miscellaneous

Apr 13, 2010

ePCR was performed for the above three mentioned SOLiD libraries using 1.5pM (180 pg/uL) of cDNA, according to the ABI “full scale” ePCR protocol. ePCRs were stored @ 4C…

<<<<<<< HEAD

Apr 13, 2010

Emulsion PCR (ePCR) was performed for the above three mentioned SOLiD libraries using 1.5pM (180 pg/uL) of cDNA, according to the ABI “full scale” ePCR protocol. ePCRs were…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

ePCR SOLiD Libraries - Abalone CC, CE pools and yellow perch CT SOLiD libraries (from 20100408)

2010

Miscellaneous

Apr 12, 2010

Emulsion PCR (ePCR) was performed for the above three mentioned SOLiD libraries using 1.5pM (180 pg/uL) of cDNA, according to the ABI “full scale” ePCR protocol. ePCRs were…

<<<<<<< HEAD

Apr 12, 2010

Amplified cDNA was cleaned up using the Invitrogen PureLink Micro Kit, but was done so according to Ambion’s Whole Transcriptome Analysis Kit protocol and then spec’d.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

cDNA clean up & Bioanalyzer for SOLiD Libraries - Abalone, Yellow Perch, Lake Trout, Herring

2010

Miscellaneous

Apr 8, 2010

Amplified cDNA was cleaned up using the Invitrogen PureLink Micro Kit, but was done so according to Ambion’s Whole Transcriptome Analysis Kit protocol and then spec’d.

<<<<<<< HEAD

Apr 8, 2010

cDNA was gel purified according to Ambion’s Whole Transcriptome Analysis Kit. The appropriate regions (100 - 200bp) were excised and cut in to 4, 1x5mm pieces. The two…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Gel Purification & PCR cDNA SOLiD Libraries - Abalone, Yellow Perch, Lake Trout, Herring

2010

Miscellaneous

Apr 7, 2010

cDNA was gel purified according to Ambion’s Whole Transcriptome Analysis Kit. The appropriate regions (100 - 200bp) were excised and cut in to 4, 1x5mm pieces. The two…

<<<<<<< HEAD

Apr 7, 2010

Samples were speedvac’d to dryness and resuspended in 3uL of nuclease-free H2O. Samples were then reversed transcribed according to Ambion’s Whole Transcriptome Analysis…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Reverse Transcription SOLiD Libraries - Abalone, Yellow Perch, Lake Trout, Herring

2010

Miscellaneous

Apr 6, 2010

Samples were speedvac’d to dryness and resuspended in 3uL of nuclease-free H2O. Samples were then reversed transcribed according to Ambion’s Whole Transcriptome Analysis…

<<<<<<< HEAD

Apr 6, 2010

All 8 samples were hybridized/ligated according to Ambion’s Whole Transcriptome Analysis Kit using Adaptor A.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Hibridizaton/Ligation SOLiD Libraries - Abalone, Yellow Perch, Lake Trout, Herring

2010

Miscellaneous

Apr 5, 2010

All 8 samples were hybridized/ligated according to Ambion’s Whole Transcriptome Analysis Kit using Adaptor A.

<<<<<<< HEAD

Apr 5, 2010

0.5uL of fragmented mRNA from each library (combined with 0.5uL) was run on Agilent Bioanalyzer 2100 using RNA Pico chips/reagents according to Agilent’s protocol.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Bioanalyzer Total, mRNA and post-fragmentation SOLiD Libraries - Abalone pools

2010

Miscellaneous

Apr 2, 2010

0.5uL of fragmented mRNA from each library (combined with 0.5uL) was run on Agilent Bioanalyzer 2100 using RNA Pico chips/reagents according to Agilent’s protocol.

<<<<<<< HEAD

Apr 2, 2010

mRNA was precipitated according to Ambion’s MicroPolyA Purist Kit protocol. Added 0.1vols of ammonium acetate, 2.5vols of 100% EtOH and incubated 30mins @ -80C. Samples were…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Precipitation and Fragmentation for SOLiD Libraries - Pooled abalone mRNA (from yesterday)

2010

Miscellaneous

Apr 1, 2010

mRNA was precipitated according to Ambion’s MicroPolyA Purist Kit protocol. Added 0.1vols of ammonium acetate, 2.5vols of 100% EtOH and incubated 30mins @ -80C. Samples were…

<<<<<<< HEAD

Apr 1, 2010

RNA of 8 samples from each group was pooled equally from each individual. RNA was precipitated according to Ambion’s MicroPolyA Purist Kit. Used 0.1 volumes of 3M NaAOc…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Precipitation & mRNA Isolation for SOLiD Libraries - Pooled abalone total RNA: Carmel control, Carmel exposed

2010

Miscellaneous

Mar 31, 2010

RNA of 8 samples from each group was pooled equally from each individual. RNA was precipitated according to Ambion’s MicroPolyA Purist Kit. Used 0.1 volumes of 3M NaAOc…

<<<<<<< HEAD

Mar 31, 2010

1uL of each sample from 20100325 was run on the Agilent 2100 Bioanalyzer on a RNA Pico 6000 chip to evaluate RNA quantity and fragmentation.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Bioanalyzer for SOLiD Libraries - Fragmented mRNA from Perch, Lake Trout & Herring RNA samples

2010

Miscellaneous

Mar 29, 2010

1uL of each sample from 20100325 was run on the Agilent 2100 Bioanalyzer on a RNA Pico 6000 chip to evaluate RNA quantity and fragmentation.

<<<<<<< HEAD

Mar 29, 2010

Fragmented mRNA according to Ambion’s Whole Transcriptome Sequencing Kit. Cleaned up sample using Ribominus Concentration Module (Invitrogen) according to Ambion’s WTS…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

SOLiD Library Prep - mRNA (perch, lake trout, herring from 20100318) Fragmentation

2010

Miscellaneous

Mar 25, 2010

Fragmented mRNA according to Ambion’s Whole Transcriptome Sequencing Kit. Cleaned up sample using Ribominus Concentration Module (Invitrogen) according to Ambion’s WTS…

<<<<<<< HEAD

Mar 25, 2010

Total and mRNA aliquots (~5ng/uL) were run on the Agilent Bioanalyzer Pico RNA chips.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Bioanalyzer for SOLiD libraries - Total and mRNA from Perch, Lake Trout & Herring RNA samples (CONTINUED from yesterday)

2010

Miscellaneous

Mar 18, 2010

Total and mRNA aliquots (~5ng/uL) were run on the Agilent Bioanalyzer Pico RNA chips.

<<<<<<< HEAD

Mar 18, 2010

mRNA was pelleted and washed according to Ambion’s MicroPolyA Purist Kit. Pellets were resuspended in 8uL nuclease-free H2O and spec’d. 0.5uL was taken from each sample…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

mRNA Precipitation for SOLiD - Perch, Lake Trout, & Herring mRNA (CONTINUED from yesterday)

2010

Miscellaneous

Mar 17, 2010

mRNA was pelleted and washed according to Ambion’s MicroPolyA Purist Kit. Pellets were resuspended in 8uL nuclease-free H2O and spec’d. 0.5uL was taken from each sample…

<<<<<<< HEAD

Mar 17, 2010

Received pooled lean and siscowet RNA from Rick. Samples will be processed immediately for SOLiD fragment libraries. Two 1.5mL snap cap tubes labelled:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

mRNA Isolation for SOLiD - Perch, Lake Trout, and Herring total RNA

2010

Miscellaneous

Mar 16, 2010

Received pooled lean and siscowet RNA from Rick. Samples will be processed immediately for SOLiD fragment libraries. Two 1.5mL snap cap tubes labelled:

<<<<<<< HEAD

Mar 16, 2010

Lexie’s PCR with this primer set and a pool of Mercenria cDNA has yielded contamination in all of her waters. Performed two sets of PCR: one with her existing primer working…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

PCR - Test Lexie’s Mercenaria 18s contamination issue

2010

Miscellaneous

Mar 10, 2010

Lexie’s PCR with this primer set and a pool of Mercenria cDNA has yielded contamination in all of her waters. Performed two sets of PCR: one with her existing primer working…

<<<<<<< HEAD

Mar 10, 2010

GSTA and DPGN primer sets used. These are duplicates based on initial differences seen between BB and DH expression. qPCR set up and plate layout here.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Mac’s BB/DH cDNA from 20091223

2010

PROPS

Jan 15, 2010

GSTA and DPGN primer sets used. These are duplicates based on initial differences seen between BB and DH expression. qPCR set up and plate layout here.

<<<<<<< HEAD

Jan 15, 2010

Continued with templated bead prep from ePCRs for these libraries. Samples were processed according to the ABI “Templated Bead Preparation Guide” following the “full-scale”…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

SOLiD Bead Titration - Herring fragmented cDNA libraries: 2LHKOD09, 4LHTOG09, 6LHPWS09

2010

Miscellaneous

Jan 14, 2010

Continued with templated bead prep from ePCRs for these libraries. Samples were processed according to the ABI “Templated Bead Preparation Guide” following the “full-scale”…

<<<<<<< HEAD

Jan 14, 2010

Using 1.5pM of starting template, based on success of the 3LHSITK09 bead prep (see 20100108).

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

SOLiD ePCRs - Herring cDNA libraries

2010

Miscellaneous

Jan 13, 2010

Using 1.5pM of starting template, based on success of the 3LHSITK09 bead prep (see 20100108).

<<<<<<< HEAD

Jan 13, 2010

Using 1.5pM of starting template, based on success of the 3LHSITK09 bead prep (see 20100108).

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

SOLiD ePCR - Herring fragmented cDNA library: 2LHKOD09

2010

Miscellaneous

Using 1.5pM of starting template, based on success of the 3LHSITK09 bead prep (see 20100108).

<<<<<<< HEAD

GNRR2 and CALL primer sets used. These are duplicates based on initial differences seen between BB and DH expression. qPCR set up and plate layout is here.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCRs - Mac’s BB/DH cDNA from 20091223

2010

PROPS

GNRR2 and CALL primer sets used. These are duplicates based on initial differences seen between BB and DH expression. qPCR set up and plate layout is here.

<<<<<<< HEAD

Completed the remainder of the procedure for template bead titration, according to the ABI “Templated Bead Preparation Guide” following the “full-scale” protocol.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

SOLiD Bead Titration - Herring fragmented cDNA library 3LHSITK09 (CONTINUED from ePCR yesterday)

2010

Miscellaneous

Jan 8, 2010

Completed the remainder of the procedure for template bead titration, according to the ABI “Templated Bead Preparation Guide” following the “full-scale” protocol.

<<<<<<< HEAD

Jan 8, 2010

Due to low yield of templated beads (12x10^6) from the first run through (see SOLiD Bead Titration below), am repeating using 1.5pM of starting template (as opposed to 0.5pM…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

SOLiD ePCR - Herring fragmented cDNA library: 3LHSITK09

2010

Miscellaneous

Due to low yield of templated beads (12x10^6) from the first run through (see SOLiD Bead Titration below), am repeating using 1.5pM of starting template (as opposed to 0.5pM…

<<<<<<< HEAD

Completed the remainder of the procedure for template bead titration, according to the ABI “Templated Bead Preparation Guide” following the “full-scale” protocol.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

SOLiD Bead Titration - Herring fragmented cDNA library 3LHSITK09(CONTINUED from ePCR yesterday)

2010

Miscellaneous

Completed the remainder of the procedure for template bead titration, according to the ABI “Templated Bead Preparation Guide” following the “full-scale” protocol.

<<<<<<< HEAD

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCRs - Tim’s Adult Gigas gill cDNA (from 20091009)

2010

Miscellaneous

<<<<<<< HEAD

Processed herring fragmented cDNA library 3LHSITK09 (88.ng/uL) according to the ABI “Templated Bead Preparation Guide” following the “full-scale” protocol. Made a 1:1000…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

SOLiD ePCR - Herring fragmented cDNA library: 3LHSITK09 (from 20091209)

2010

Miscellaneous

Processed herring fragmented cDNA library 3LHSITK09 (88.ng/uL) according to the ABI “Templated Bead Preparation Guide” following the “full-scale” protocol. Made a 1:1000…

<<<<<<< HEAD

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCRs - Tim’s Adult Gigas gill cDNA (from 20091009)

2010

Miscellaneous

Jan 5, 2010

<<<<<<< HEAD

Jan 5, 2010

qPCR was set up on these cDNAs using the following primers:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - BB & DH cDNA (from 20091223)

2009

PROPS

Dec 31, 2009

qPCR was set up on these cDNAs using the following primers:

<<<<<<< HEAD

Dec 31, 2009

qPCR was set up on these cDNAs using the following primers:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCRs - BB & DH cDNA (from 20091223)

2009

PROPS

Dec 30, 2009

qPCR was set up on these cDNAs using the following primers:

<<<<<<< HEAD

Dec 30, 2009

qPCR was set up on these cDNAs using the following primers:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - BB & DH cDNA (from 20091223)

2009

PROPS

qPCR was set up on these cDNAs using the following primers:

<<<<<<< HEAD

Juvenile sockeye salmon were subjected to initial heat stress of 18C. 10 fish were weighed, measured and then snap frozen in LN2. Samples were transferred to a freezer box…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Alaska sockeye salmon sampling (with Seebs): Family #13

2009

Miscellaneous

Juvenile sockeye salmon were subjected to initial heat stress of 18C. 10 fish were weighed, measured and then snap frozen in LN2. Samples were transferred to a freezer box…

<<<<<<< HEAD

qPCR was set up on these cDNAs using the following primers:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - BB & DH cDNA (from 20091223) and Emma primer sets for testing

2009

PROPS

qPCR was set up on these cDNAs using the following primers:

<<<<<<< HEAD

qPCR was set up on these cDNAs using the following primers:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCRs - BB & DH cDNA (from 20091223)

2009

PROPS

Dec 28, 2009

qPCR was set up on these cDNAs using the following primers:

<<<<<<< HEAD

Dec 28, 2009

qPCR was set up on these cDNAs using the following primers:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCRs - BB & DH cDNA (from yesterday)

2009

PROPS

Dec 24, 2009

qPCR was set up on these cDNAs using the following primers:

<<<<<<< HEAD

Dec 24, 2009

Samples were submitted for sequencing. Mac prepped all Roberts Lab samples excluding the Opsin VMC gel slice 2 from 20091217-02. The gel slice was purified with Millipore…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Sequencing - Mac methylation samples, Sam rhodopsin samples, Lisa samples

2009

Miscellaneous

Samples were submitted for sequencing. Mac prepped all Roberts Lab samples excluding the Opsin VMC gel slice 2 from 20091217-02. The gel slice was purified with Millipore…

<<<<<<< HEAD

qPCR was set up on these cDNAs using HMGP_5’/3’ and SPI_5’/3’ primers. qPCR set up and plate layout can be found here.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - BB & DH cDNA (from earlier today)

2009

PROPS

qPCR was set up on these cDNAs using HMGP_5’/3’ and SPI_5’/3’ primers. qPCR set up and plate layout can be found here.

<<<<<<< HEAD

Made a fresh, double batch (50uL rxn instead of 25uL) of cDNA according to Promega MMLV protocol using oligo dT primers. cDNA was put into a plate for faster qPCR loading. cD…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Reverse Transcription - BB & DH DNased RNA (from 20090514)

2009

PROPS

Made a fresh, double batch (50uL rxn instead of 25uL) of cDNA according to Promega MMLV protocol using oligo dT primers. cDNA was put into a plate for faster qPCR loading. cD…

<<<<<<< HEAD

This is an exact repeat of the PCR from yesterday, due to inconsistencies between repeated PCRs from yesterday and earlier today. Here’s yesterday’s workup

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

PCR - Sepia cDNA

2009

Miscellaneous

Dec 17, 2009

This is an exact repeat of the PCR from yesterday, due to inconsistencies between repeated PCRs from yesterday and earlier today. Here’s yesterday’s workup

<<<<<<< HEAD

Dec 17, 2009

This is an exact repeat of the PCR from yesterday, due to inconsistencies between repeated PCRs from yesterday and earlier today. Here’s yesterday’s workup. Samples were…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

PCR - Sepia cDNA

2009

Miscellaneous

This is an exact repeat of the PCR from yesterday, due to inconsistencies between repeated PCRs from yesterday and earlier today. Here’s yesterday’s workup. Samples were…

<<<<<<< HEAD

Set up PCR on recent Sepia cDNA and DNased RNA samples using both S. officianalis_rhodopsin_F, R primers & Sep_op_F2, R2 primers. After yesterday’s intirguing PCR results…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

PCR - Sepia cDNA and DNased RNA

2009

Miscellaneous

Set up PCR on recent Sepia cDNA and DNased RNA samples using both S. officianalis_rhodopsin_F, R primers & Sep_op_F2, R2 primers. After yesterday’s intirguing PCR results…

<<<<<<< HEAD

Set up PCR on recent Sepia cDNA samples using both S. officianalis_rhodopsin_F, R primers & Sep_op_F2, R2 primers. PCR set up is here. Looking back at my old paper (gasp!)…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

PCR - Sepia cDNA (from yesterday)

2009

Miscellaneous

Set up PCR on recent Sepia cDNA samples using both S. officianalis_rhodopsin_F, R primers & Sep_op_F2, R2 primers. PCR set up is here. Looking back at my old paper (gasp!)…

<<<<<<< HEAD

Spec - DNased Abalone 07:12 RNA

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Reverse Transcription - Abalone 07:12 DNased RNA (from 20090623)

2009

Miscellaneous

Spec - DNased Abalone 07:12 RNA

<<<<<<< HEAD

DNase Treatment - Sepia RNA (from 20091204)

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Reverse Transcription - Sepia DNased RNA

2009

Miscellaneous

Dec 14, 2009

DNase Treatment - Sepia RNA (from 20091204)

<<<<<<< HEAD

Dec 14, 2009

Samples were run on the DNA 1000 chip for cDNA smear analysis.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Bioanalyzer - Herring Liver cDNA for SOLiD Libraries

2009

Miscellaneous

Dec 11, 2009

Samples were run on the DNA 1000 chip for cDNA smear analysis.

<<<<<<< HEAD

Dec 11, 2009

Emulsion PCR was performed with the two inner gel bands cut out earlier today according to the Ambio WTK protocol. PCR was run for 15 cycles. After the PCR, the samples were…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Emulsion PCR - Herring Liver cDNA for SOLiD Libraries

2009

Miscellaneous

Emulsion PCR was performed with the two inner gel bands cut out earlier today according to the Ambio WTK protocol. PCR was run for 15 cycles. After the PCR, the samples were…

<<<<<<< HEAD

Ligation reactions from yesterday were subject to reverse transcription according to protocol. Master mix workup info is here. Samples were incubated @ 42C, 30mins and then…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Reverse Transcription - Herring Liver mRNA for SOLiD Libraries

2009

Miscellaneous

Ligation reactions from yesterday were subject to reverse transcription according to protocol. Master mix workup info is here. Samples were incubated @ 42C, 30mins and then…

<<<<<<< HEAD

RNA from yesterday was speedvac’d to dryness and resuspended in 3uL of nuclease-free H2O. Samples were mixed with Adaptor Mix A and hybridized according to Ambion WTK…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Adapter Hybridization and Ligation - Herring Liver mRNA for SOLiD Libraries

2009

Miscellaneous

Dec 8, 2009

RNA from yesterday was speedvac’d to dryness and resuspended in 3uL of nuclease-free H2O. Samples were mixed with Adaptor Mix A and hybridized according to Ambion WTK…

<<<<<<< HEAD

Dec 8, 2009

Samples from 20091203. 0.5uL was removed from each and transferred to separate tubes and diluted to < 5ng/uL for subsequent Bioanalyzer analysis using the Pico chip. Samples…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Fragmentation - Herring Liver mRNA for SOLiD Libraries

2009

Miscellaneous

Dec 7, 2009

Samples from 20091203. 0.5uL was removed from each and transferred to separate tubes and diluted to < 5ng/uL for subsequent Bioanalyzer analysis using the Pico chip. Samples…

<<<<<<< HEAD

Dec 7, 2009

Isolated RNA from 7 sepia samples received 20091125. Samples were removed from RNA Later, blotted and homogenized in 500uL of TriReagent. 500uL of additional TriReagent was…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation - Sepia samples

2009

Miscellaneous

Dec 4, 2009

Isolated RNA from 7 sepia samples received 20091125. Samples were removed from RNA Later, blotted and homogenized in 500uL of TriReagent. 500uL of additional TriReagent was…

<<<<<<< HEAD

Dec 4, 2009

Submitted 1.5 plates for Sanger sequencing. Dungan isolates prepared by me, Lake Trout HRM prepared by Rony and Emma’s differential display cloning samples prepared by her.…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Sequencing - Dungan Isolates, Lake Trout HRM and Emma DD cloning

2009

Miscellaneous

Submitted 1.5 plates for Sanger sequencing. Dungan isolates prepared by me, Lake Trout HRM prepared by Rony and Emma’s differential display cloning samples prepared by her.…

<<<<<<< HEAD

Spun samples 16,000g, 30mins, 4C. Discarded supe, quick spun tubes, removed residual supe, washed with 1mL 70% EtOH. Spun samples 16,000g, 15mins, 4C. Discarded supe, quick…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

mRNA Precipitation - Herring Liver mRNA for SOLiD Libraries (continued from yesterday)

2009

Miscellaneous

Spun samples 16,000g, 30mins, 4C. Discarded supe, quick spun tubes, removed residual supe, washed with 1mL 70% EtOH. Spun samples 16,000g, 15mins, 4C. Discarded supe, quick…

<<<<<<< HEAD

All clams appeared to be alive and well. Most had their siphons out when I arrived to start collecting tissues. Clams were shucked after 24hr challenge. Gill and mantle…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Hard Clam Challenge - QPX Strain S-1 (continued from yesterday)

2009

Miscellaneous

All clams appeared to be alive and well. Most had their siphons out when I arrived to start collecting tissues. Clams were shucked after 24hr challenge. Gill and mantle…

<<<<<<< HEAD

Samples were pelleted for 30mins, 16,000g @ 4C. Supe was discarded, samples quick spun, residual supe removed and then washed with 1mL 70% EtOH. Tubes were vortexed until…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Precipitation - Herring Liver RNA for SOLiD Libraries (continued from yesterday)

2009

Miscellaneous

Samples were pelleted for 30mins, 16,000g @ 4C. Supe was discarded, samples quick spun, residual supe removed and then washed with 1mL 70% EtOH. Tubes were vortexed until…

<<<<<<< HEAD

50uL of RNA from each of the following were precipitated O/N @ -20C:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Precipitation - Herring Liver RNA for SOLiD Libraries

2009

Miscellaneous

50uL of RNA from each of the following were precipitated O/N @ -20C:

<<<<<<< HEAD

Challenged 2 FL hard clams and 1 BX hard clam with ~100uL of unwashed, 11 day old cultures. 2 FL hard clams and 1 BX hard clam received ~100uL of QPX media, as controls.…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Hard Clam Challenge - QPX Strain S-1

2009

Miscellaneous

Challenged 2 FL hard clams and 1 BX hard clam with ~100uL of unwashed, 11 day old cultures. 2 FL hard clams and 1 BX hard clam received ~100uL of QPX media, as controls.…

<<<<<<< HEAD

Received samples from Scott Lindell today. Two Ziplock bags taped together labelled “11/16/09 Clams scudders.” The bags contain 2mL screw cap tubes with small tissue samples…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

MBL Shipment - Hard Clam gill tissue in RNA Later

2009

Miscellaneous

Received samples from Scott Lindell today. Two Ziplock bags taped together labelled “11/16/09 Clams scudders.” The bags contain 2mL screw cap tubes with small tissue samples…

<<<<<<< HEAD

Received sepia tissue samples in RNA Later from Kendra Buresch. Here’s the list of tissue we received, according to the Post-It with the samples:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

MBL Shipment - Sepia tissue samples

2009

Miscellaneous

Nov 25, 2009

Received sepia tissue samples in RNA Later from Kendra Buresch. Here’s the list of tissue we received, according to the Post-It with the samples:

<<<<<<< HEAD

Nov 25, 2009

Received hard clams from Scott Lindell today. Two bags. One group (4 live clams, 1 empty shell) labelled as “FL” and another group (9 live clams) labelled as “BX.” Clams…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

MBL Shipment - Hard Clams

2009

Miscellaneous

Nov 24, 2009

Received hard clams from Scott Lindell today. Two bags. One group (4 live clams, 1 empty shell) labelled as “FL” and another group (9 live clams) labelled as “BX.” Clams…

<<<<<<< HEAD

Nov 24, 2009

Data from MoGene was received today on two DVDs and one HDD. Data is two runs of two libraries, due to MoGene concerns that the data of the first run looked bad (too few…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Herring 454 Data

2009

Miscellaneous

Data from MoGene was received today on two DVDs and one HDD. Data is two runs of two libraries, due to MoGene concerns that the data of the first run looked bad (too few…

<<<<<<< HEAD

Received a shipment of various MV oysters/cod samples from Scott Lindell at MBL. However, these were NOT shipped on dry ice! Samples were put @ -80C. Will be organized at a…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

MBL Shipment - MV oysters/cod

2009

Miscellaneous

Received a shipment of various MV oysters/cod samples from Scott Lindell at MBL. However, these were NOT shipped on dry ice! Samples were put @ -80C. Will be organized at a…

<<<<<<< HEAD

This is a repeat of yesterday’s set up with LABY primers, but with an annealing temp of 53C in hopes of improving the number of amplicons generated from additional samples.…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

PCR - “Unknown” Dungans/Lyons

2009

Miscellaneous

Nov 18, 2009

This is a repeat of yesterday’s set up with LABY primers, but with an annealing temp of 53C in hopes of improving the number of amplicons generated from additional samples.…

<<<<<<< HEAD

Nov 18, 2009

This was done on the numbered tubes using the LABY A/Y primers for eventual sequencing. Turns out many of the tubes have some info (other than just a number) on their sides…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

PCR - “Unkown” Dungans/Lyons

2009

Miscellaneous

Nov 17, 2009

This was done on the numbered tubes using the LABY A/Y primers for eventual sequencing. Turns out many of the tubes have some info (other than just a number) on their sides…

<<<<<<< HEAD

Nov 17, 2009

Received Hard Clam gill samples on “wet ice” in RNA Later from Rutgers. Samples were collected on 11/4/09 (clams held in refrigerator) and preserved (gill tissue collected)…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Hard Clams - Shipment from Rutgers

2009

Miscellaneous

Nov 13, 2009

Received Hard Clam gill samples on “wet ice” in RNA Later from Rutgers. Samples were collected on 11/4/09 (clams held in refrigerator) and preserved (gill tissue collected)…

<<<<<<< HEAD

Nov 13, 2009

This is a second submission of 12 individuals from 8 primer sets. The previous sequencing run was botched because I used the combined primer plate instead of a single…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Sequencing - Lake Trout HRM

2009

Miscellaneous

Nov 10, 2009

This is a second submission of 12 individuals from 8 primer sets. The previous sequencing run was botched because I used the combined primer plate instead of a single…

<<<<<<< HEAD

Nov 10, 2009

See Rachel’s 441 Notebook from 10/28/2009 through 11/4/2009 for experiment info. 500mL of water was collected from the CO2 and the air tanks. Water was vacuum filtered…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Oyster CO2/Mechanical Stress - Water quality

2009

Miscellaneous

Nov 5, 2009

See Rachel’s 441 Notebook from 10/28/2009 through 11/4/2009 for experiment info. 500mL of water was collected from the CO2 and the air tanks. Water was vacuum filtered…

<<<<<<< HEAD

Nov 5, 2009

Submitted 400ng of liver mRNA (SR01) and 400ng of testes (gonad) mRNA (SR02) to MoGene. Samples were packed in dry ice and FedEx.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Sample Submissions to MoGene for 454 Analysis - Herring Liver and Testes mRNA

2009

Miscellaneous

Samples Submitted

Submitted 400ng of liver mRNA (SR01) and 400ng of testes (gonad) mRNA (SR02) to MoGene. Samples were packed in dry ice and FedEx.

<<<<<<< HEAD

Sample was spun 16,000g, 30mins, 4C. Supe removed. Pellet washed with 1mL 70% EtOH. Spun 16,000g, 10mins, 4C. Supe removed. Pellet resuspended in 250uL of nuclease free H2O.…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

mRNA Isolation - Herring gonad/ovary RNA (from 20091023)

2009

Miscellaneous

Sample was spun 16,000g, 30mins, 4C. Supe removed. Pellet washed with 1mL 70% EtOH. Spun 16,000g, 10mins, 4C. Supe removed. Pellet resuspended in 250uL of nuclease free H2O.…

<<<<<<< HEAD

A subset (3 samples from each group) of samples were pooled (see spreadsheet, green-highlighted samples), each providing ~7.5ug of RNA, yielding 112.17uL. 0.1 vols of 3M…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Precipitation - Herring gonad/ovary RNA (from 20091023)

2009

Miscellaneous

A subset (3 samples from each group) of samples were pooled (see spreadsheet, green-highlighted samples), each providing ~7.5ug of RNA, yielding 112.17uL. 0.1 vols of 3M…

<<<<<<< HEAD

Isolated mRNA using Ambion’s MicroPolyA Purist Kit according to protocol. Performed two rounds of isolation to decrease residual rRNA carryover that we frequently see after…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

mRNA Isolation - Herring Liver RNA (from 20091021)

2009

Miscellaneous

Isolated mRNA using Ambion’s MicroPolyA Purist Kit according to protocol. Performed two rounds of isolation to decrease residual rRNA carryover that we frequently see after…

<<<<<<< HEAD

A subset of samples (4 samples from each group) were pooled (see spreadsheet, green-highlighted samples), each providing ~68ug of RNA. The pooled sample was split into two…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Precipitation - Herring Liver Samples

2009

Miscellaneous

A subset of samples (4 samples from each group) were pooled (see spreadsheet, green-highlighted samples), each providing ~68ug of RNA. The pooled sample was split into two…

<<<<<<< HEAD

RNA was isolated according to protocol. Pellets were resuspended in 50uL of 0.1%DEPC-H2O, heated @ 55C for 5 mins, spec’d and stored @ -80C in the “Herring RNA Box #1”.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation - Herring Gonad/Ovary Samples

2009

Miscellaneous

RNA was isolated according to protocol. Pellets were resuspended in 50uL of 0.1%DEPC-H2O, heated @ 55C for 5 mins, spec’d and stored @ -80C in the “Herring RNA Box #1”.

<<<<<<< HEAD

From the Seeb Lab. Homogenized entire gonad/ovary samples in 5mL of TriReagent with the sonicator. In essence, based on the manufacturer’s recommendation, this means the…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation - Herring Gonad/Ovary Samples

2009

Miscellaneous

Oct 22, 2009

From the Seeb Lab. Homogenized entire gonad/ovary samples in 5mL of TriReagent with the sonicator. In essence, based on the manufacturer’s recommendation, this means the…

<<<<<<< HEAD

Oct 22, 2009

RNA was isolated according to protocol. Pellets were resuspended in 200uL of 0.1%DEPC-H2O, heated @ 55C for 5 mins, spec’d and stored @ -80C in the “Herring RNA Box #1”.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation - Herring Liver Samples

2009

Miscellaneous

Oct 21, 2009

RNA was isolated according to protocol. Pellets were resuspended in 200uL of 0.1%DEPC-H2O, heated @ 55C for 5 mins, spec’d and stored @ -80C in the “Herring RNA Box #1”.

<<<<<<< HEAD

Oct 21, 2009

From Seeb Lab. Homogenized entire liver samples in 5mL of TriReagent with the Tissue Tearers. In essence, based on the manufacturer’s recommendation, this means the ratio of…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation - Herring Liver Samples (LHPWS09 1-6)

2009

Miscellaneous

Oct 20, 2009

From Seeb Lab. Homogenized entire liver samples in 5mL of TriReagent with the Tissue Tearers. In essence, based on the manufacturer’s recommendation, this means the ratio of…

<<<<<<< HEAD

Oct 20, 2009

Set up qPCR with Cg_P450 primers and TNFRAF3’/5’ primers. Plate layout/setup is here.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCRs - Tim’s adult gigas challenge cDNA (from 20091009)

2009

Miscellaneous

Oct 13, 2009

Set up qPCR with Cg_P450 primers and TNFRAF3’/5’ primers. Plate layout/setup is here.

<<<<<<< HEAD

Oct 13, 2009

Set up qPCR with Cg_HIF1 (hypoxia induced factor 1) primers and prostaglandin E2 primers. Plate layout/setup is here.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Tim’s adult gigas challenge cDNA (from 20091009)

2009

Miscellaneous

Oct 12, 2009

Set up qPCR with Cg_HIF1 (hypoxia induced factor 1) primers and prostaglandin E2 primers. Plate layout/setup is here.

<<<<<<< HEAD

Oct 12, 2009

Set up qPCR with EF1 primers and IL17 Internal primers. Plate layout/setup is here. Note: gDNA sample used as a “positive” control will NOT amplify with the EF1 primers.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Tim’s adult gigas challenge cDNA (from today)

2009

Miscellaneous

Set up qPCR with EF1 primers and IL17 Internal primers. Plate layout/setup is here. Note: gDNA sample used as a “positive” control will NOT amplify with the EF1 primers.

<<<<<<< HEAD

Performed RT rxns. Setup is here. cDNA was subsequently diluted 1:4 (added 75uL H2O to each well) to properly mirror Tim’s previous qPCRs.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Reverse Transcription - Tim’s adult gigas challenge DNased RNA (from 20091008)

2009

Miscellaneous

Performed RT rxns. Setup is here. cDNA was subsequently diluted 1:4 (added 75uL H2O to each well) to properly mirror Tim’s previous qPCRs.

<<<<<<< HEAD

Performed qPCR using q18s primers on re-DNased RNA (1:100 dilution to match final concentration of template after making cDNA). qPCR set up and plate layout are here.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Tim’s adults gigas challenge re-DNased RNA (from today)

2009

Miscellaneous

Performed qPCR using q18s primers on re-DNased RNA (1:100 dilution to match final concentration of template after making cDNA). qPCR set up and plate layout are here.

<<<<<<< HEAD

5 samples from yesterday’s treatment still came up on qPCR, so I will re-DNase those 5 samples. Followed standard protocol in Ambion’s Turbo DNA-free kit.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNase Treatment - Re-DNase of Tim’s adult gigas challenge RNA (from yesterday)

2009

Miscellaneous

5 samples from yesterday’s treatment still came up on qPCR, so I will re-DNase those 5 samples. Followed standard protocol in Ambion’s Turbo DNA-free kit.

<<<<<<< HEAD

Previous qPCR was done incorrectly (wrong primers), so am repeating with the correct primers. Performed qPCR using q18s primers on DNased RNA (1:100 dilution to match final…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Tim’s adults gigas challenge DNased RNA (from today)

2009

Miscellaneous

Previous qPCR was done incorrectly (wrong primers), so am repeating with the correct primers. Performed qPCR using q18s primers on DNased RNA (1:100 dilution to match final…

<<<<<<< HEAD

Performed qPCR using q18s primers on DNased RNA (1:100 dilution to match final concentration of template after making cDNA). qPCR set up and plate layout are here.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Tim’s adults gigas challenge DNased RNA (from today)

2009

Miscellaneous

Performed qPCR using q18s primers on DNased RNA (1:100 dilution to match final concentration of template after making cDNA). qPCR set up and plate layout are here.

<<<<<<< HEAD

Used 5uL of RNA from each sample, brought samples up to 50uL with H2O and treated according to Ambion’s Turbo DNA-free kit. Rigorous protocol was followed (1.5uL DNase…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNase Treatment - Tim’s adult gigas challenge RNA (from 20090930)

2009

Miscellaneous

Used 5uL of RNA from each sample, brought samples up to 50uL with H2O and treated according to Ambion’s Turbo DNA-free kit. Rigorous protocol was followed (1.5uL DNase…

<<<<<<< HEAD

Samples were delivered for analysis on the DNA 1000 chip.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Bioanalyzer Submission - Trout RBC, Colleen’s gigas GE sample, Mac’s DH/BB PCR for SOLiD WTK

2009

Miscellaneous

Oct 7, 2009

Samples were delivered for analysis on the DNA 1000 chip.

<<<<<<< HEAD

Oct 7, 2009

The four samples from yesterday were prepared according to the Agilent SOLiD WTK protocol. Briefly:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Reverse Transcription/cDNA purification/Emulsion PCR - Ligation rxns of trout fragmented RNA for SOLiD WTK (from yesterday)

2009

Miscellaneous

Oct 6, 2009

The four samples from yesterday were prepared according to the Agilent SOLiD WTK protocol. Briefly:

<<<<<<< HEAD

Oct 6, 2009

See the Next Gen Seq Library Database for more info. Processed the 4 samples (one set Ribominus only, one set Ribominus + PolyA enriched) according to the Agilent WTK.…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Adapter Ligation - Rick’s trout fragmented control/poly I:C samples for SOLiD WTK

2009

Miscellaneous

See the Next Gen Seq Library Database for more info. Processed the 4 samples (one set Ribominus only, one set Ribominus + PolyA enriched) according to the Agilent WTK.…

<<<<<<< HEAD

Performed qPCR using q18s primers on DNased RNA (1:100 dilution to match final concentration of template after making cDNA). qPCR set up and plate layout are here.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Tim’s adults gigas challenge DNased RNA (from 20091002)

2009

Miscellaneous

Performed qPCR using q18s primers on DNased RNA (1:100 dilution to match final concentration of template after making cDNA). qPCR set up and plate layout are here.

<<<<<<< HEAD

Used 5uL of RNA from each sample, brought samples up to 50uL with H2O and treated according to Ambion’s Turbo DNA-free kit. Transferred treated samples to a PCR plate to…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNase Treatment - Tim’s adult gigas challenge RNA (from 20090930)

2009

Miscellaneous

Oct 2, 2009

Used 5uL of RNA from each sample, brought samples up to 50uL with H2O and treated according to Ambion’s Turbo DNA-free kit. Transferred treated samples to a PCR plate to…

<<<<<<< HEAD

Oct 2, 2009

Ran qPCR on RNA to evaluate gDNA contamination in the samples. Dilutions of the RNA were made at 1:100, which would be the equivalent amount when making cDNA (1:25) and…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCRs - Check gDNA contamination with EF1 & 18s primers in gigas gill RNA (from yesterday)

2009

Miscellaneous

Oct 1, 2009

Ran qPCR on RNA to evaluate gDNA contamination in the samples. Dilutions of the RNA were made at 1:100, which would be the equivalent amount when making cDNA (1:25) and…

<<<<<<< HEAD

Oct 1, 2009

RNA was isolated using 500uL of TriReagent for all samples. Samples were resuspended in 100uL of 0.1%DEPC-H2O and spec’d. Samples stored in Tim’s “NAME OF BOX” box.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation - Tim’s adult gigas challenge samples

2009

Miscellaneous

Sep 30, 2009

RNA was isolated using 500uL of TriReagent for all samples. Samples were resuspended in 100uL of 0.1%DEPC-H2O and spec’d. Samples stored in Tim’s “NAME OF BOX” box.

<<<<<<< HEAD

Sep 30, 2009

Submitted Rick’s trout RBC samples to FHRC for bioanalysis using the PicoChip for use with the SOLiD WTK. Submission sheet is here (dead link - linked to 20090929-01.jpg on…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Bioanalyzer Submission - Rick’s trout RBC samples (various dates)

2009

Miscellaneous

Submitted Rick’s trout RBC samples to FHRC for bioanalysis using the PicoChip for use with the SOLiD WTK. Submission sheet is here (dead link - linked to 20090929-01.jpg on…

<<<<<<< HEAD

Continued precipitation. Spun samples 30 mins, 16,000g, 4C. Removed supe. Added 1mL 70% EtOH. Spun samples 15mins, 16,000g, 4C. Removed supe. Resuspended in 8uL H2O.…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Fragmentation - Rick’s trout RBC samples prepped earlier today

2009

Miscellaneous

Continued precipitation. Spun samples 30 mins, 16,000g, 4C. Removed supe. Added 1mL 70% EtOH. Spun samples 15mins, 16,000g, 4C. Removed supe. Resuspended in 8uL H2O.…

<<<<<<< HEAD

The “control” and “poly I:C” samples prepared earlier today were EtOH precipitated in preparation for fragmentation.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

EtOH Precipitation - Rick’s trout Ribosomoal-depleted RNA for SOLiD WTK (from today)

2009

Miscellaneous

The “control” and “poly I:C” samples prepared earlier today were EtOH precipitated in preparation for fragmentation.

<<<<<<< HEAD

Prior to starting the procedure, 0.5uL of total RNA was removed from each sample (control, polyI:C), diluted to ~5ng/uL. 1.5uL of each of these was transferred to a 0.5mL…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Ribosomal-depleted RNA - Rick’s trout RBC samples for the SOLiD WTK

2009

Miscellaneous

Prior to starting the procedure, 0.5uL of total RNA was removed from each sample (control, polyI:C), diluted to ~5ng/uL. 1.5uL of each of these was transferred to a 0.5mL…

<<<<<<< HEAD

Samples were fragmented according to the Whole Transcriptome Kit protocol. Samples were then cleaned up using Invitrogen’s Modified RiboMinus Concentration Module, according…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Fragmentation - Rick’s trout RBC samples prepped earlier today (see below)

2009

Miscellaneous

Samples were fragmented according to the Whole Transcriptome Kit protocol. Samples were then cleaned up using Invitrogen’s Modified RiboMinus Concentration Module, according…

<<<<<<< HEAD

Was given ~0.5ug of each of these two RNA samples and processed them with Ambion’s microPolyA Purist Kit according to protocol. After elution, the samples were EtOH…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

mRNA Isolation - Rick’s trout RBC samples previously treated with Ribominus Kit (by Mac)

2009

Miscellaneous

Was given ~0.5ug of each of these two RNA samples and processed them with Ambion’s microPolyA Purist Kit according to protocol. After elution, the samples were EtOH…

<<<<<<< HEAD

Was given ~0.5ug of each of these two RNA samples and processed them with Ambion’s microPolyA Purist Kit according to protocol. After elution, the samples were EtOH…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

mRNA Isolation - Gigas BB and DH samples previously treated with Ribominus Kit (by Mac)

2009

Miscellaneous

Sep 18, 2009

Was given ~0.5ug of each of these two RNA samples and processed them with Ambion’s microPolyA Purist Kit according to protocol. After elution, the samples were EtOH…

<<<<<<< HEAD

Sep 18, 2009

Was given 1ug of each of these two RNA samples and processed them with Promega’s PolyA Tract Kit according to protocol. After elution, the samples were EtOH precipitated @…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

mRNA Isolation - Gigas BB and DH samples previously treated with Ribominus Kit (by Mac)

2009

Miscellaneous

Sep 16, 2009

Was given 1ug of each of these two RNA samples and processed them with Promega’s PolyA Tract Kit according to protocol. After elution, the samples were EtOH precipitated @…

<<<<<<< HEAD

Sep 16, 2009

The following primers from primer plate LTP01 will be used for analysis of Rick’s Lake Trout DNA1 plate (from 4/28/2009): G10, C11, H11, A12. HRM set up is here. It is the…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

HRMs - Lake Trout SNPs (HRM_white-05 & HRM_white_06)

2009

Miscellaneous

Sep 15, 2009

The following primers from primer plate LTP01 will be used for analysis of Rick’s Lake Trout DNA1 plate (from 4/28/2009): G10, C11, H11, A12. HRM set up is here. It is the…

<<<<<<< HEAD

Sep 15, 2009

The following primers from primer plate LTP01 will be used for analysis of Rick’s Lake Trout DNA1 plate (from 4/28/2009): E4, B5, A7, D7. HRM set up is here. It is the same…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

HRMs - Lake Trout SNPs (HRM_white-03 & HRM_white-04)

2009

Miscellaneous

Sep 10, 2009

The following primers from primer plate LTP01 will be used for analysis of Rick’s Lake Trout DNA1 plate (from 4/28/2009): E4, B5, A7, D7. HRM set up is here. It is the same…

<<<<<<< HEAD

Sep 10, 2009

The following primers from primer plate LTP01 will be used for analysis of Rick’s Lake Trout DNA plate (from 4/28/2009): A3, D3, G3, A4. HRM set up is here. It is the same…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

HRM - Lake Trout SNPs (HRM_white-02)

2009

Miscellaneous

Sep 9, 2009

The following primers from primer plate LTP01 will be used for analysis of Rick’s Lake Trout DNA plate (from 4/28/2009): A3, D3, G3, A4. HRM set up is here. It is the same…

<<<<<<< HEAD

Sep 9, 2009

The following primers from primer plate LTP01 will be used for analysis of Rick’s Lake Trout DNA plate (from 4/28/2009): A1, C1, H1, B2. So, that’s 4 primer sets x 96 DNA…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

HRM - Lake Trout SNPs (HRM-white-01)

2009

Miscellaneous

Sep 3, 2009

The following primers from primer plate LTP01 will be used for analysis of Rick’s Lake Trout DNA plate (from 4/28/2009): A1, C1, H1, B2. So, that’s 4 primer sets x 96 DNA…

<<<<<<< HEAD

Sep 3, 2009

Tested out the plate of Lake Trout primers (LTP01 - forward and reverse combined) for SNP detection. qPCR was performed using Roche 2x HRM M.M. qPCR set up is here. Cycling…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - HRM Lake Trout SNP primer test

2009

Miscellaneous

Sep 1, 2009

Tested out the plate of Lake Trout primers (LTP01 - forward and reverse combined) for SNP detection. qPCR was performed using Roche 2x HRM M.M. qPCR set up is here. Cycling…

<<<<<<< HEAD

Sep 1, 2009

The two primer plates (LTP01F, LTP01R) were received today. Primers (supplied as 10 nmoles of each) will be reconstituted with 100uL of PCR H2O to make a Cf of 100uM.…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Primers - Lake Trout Primers for HRM

2009

Miscellaneous

The two primer plates (LTP01F, LTP01R) were received today. Primers (supplied as 10 nmoles of each) will be reconstituted with 100uL of PCR H2O to make a Cf of 100uM.…

<<<<<<< HEAD

Master mix containing Gigas gDNA will be used to verify that the recalibration did work. qPCR setup/plate layout is here. I’ve made a master mix using Cg_HSP70_F/R primers…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Gigas gDNA test of recalibrated Opticon 2

2009

Miscellaneous

Master mix containing Gigas gDNA will be used to verify that the recalibration did work. qPCR setup/plate layout is here. I’ve made a master mix using Cg_HSP70_F/R primers…

<<<<<<< HEAD

According to the Bio-Rad rep that analyzed the calibration test on 20090824, recalibration might be a good idea. As such, we’ll do that. Old calibration file was found and…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Recalibration of Opticon 2

2009

Miscellaneous

According to the Bio-Rad rep that analyzed the calibration test on 20090824, recalibration might be a good idea. As such, we’ll do that. Old calibration file was found and…

<<<<<<< HEAD

Sample was removed from -20C and spun @ 4C, 16,000 x g for 30mins. Supe removed, pellet washed with 1mL 70% EtOH and spun @ 4C, 16,000 x g for 15mins. Supe removed, tube…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Precipitation - C.pugetti DNA for JGI submission (continued from yesterday)

2009

Miscellaneous

Sample was removed from -20C and spun @ 4C, 16,000 x g for 30mins. Supe removed, pellet washed with 1mL 70% EtOH and spun @ 4C, 16,000 x g for 15mins. Supe removed, tube…

<<<<<<< HEAD

Precipitate DNA from 20090526 to concentrate and run on gel for resubmission to JGI to see what happens. Added 0.1 volume of 3M sodium acetate, pH = 5.2 (40uL) and 2 volumes…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Precipitation - C.pugetti DNA for JGI submission

2009

Miscellaneous

Aug 25, 2009

Precipitate DNA from 20090526 to concentrate and run on gel for resubmission to JGI to see what happens. Added 0.1 volume of 3M sodium acetate, pH = 5.2 (40uL) and 2 volumes…

<<<<<<< HEAD

Aug 25, 2009

Based on recs from Bio-Rad rep (Carl Fisher), will repeat Opticon 2 calibration (see 20090813) test according to Opticon manual. Then, will rotate plate 180 degrees and…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Additional Calibration test of Opticon 2

2009

Miscellaneous

Aug 24, 2009

Based on recs from Bio-Rad rep (Carl Fisher), will repeat Opticon 2 calibration (see 20090813) test according to Opticon manual. Then, will rotate plate 180 degrees and…

<<<<<<< HEAD

Aug 24, 2009

Ran a qPCR on Rick’s Lake Trout DNA from 4/28/2009 using primers in Carita’s CMA01 Primer Plate (Excel file). DNA was pooled (2uL from each sample), spec’d and diluted to…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Carita Primer Test for High Resolution Melt (HRM) Curve Analysis

2009

Miscellaneous

Aug 17, 2009

Ran a qPCR on Rick’s Lake Trout DNA from 4/28/2009 using primers in Carita’s CMA01 Primer Plate (Excel file). DNA was pooled (2uL from each sample), spec’d and diluted to…

<<<<<<< HEAD

Aug 17, 2009

Received new FAM calibration reagent. It comes pre-prepared in a 1x PCR buffer (0.3uM), however there is only enough for a single plate (use 50uL/well). Will run plate in…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Calibration test of Opticon 2

2009

Miscellaneous

Aug 13, 2009

Received new FAM calibration reagent. It comes pre-prepared in a 1x PCR buffer (0.3uM), however there is only enough for a single plate (use 50uL/well). Will run plate in…

<<<<<<< HEAD

Aug 13, 2009

Due to results of Opticon testing from 20090722, we have acquired FAM Calibartion Dye from Bio-Rad. Although not listed online or on the product itself, Bio-Rad customer…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Calibration test of Opticon 2

2009

Miscellaneous

Aug 6, 2009

Due to results of Opticon testing from 20090722, we have acquired FAM Calibartion Dye from Bio-Rad. Although not listed online or on the product itself, Bio-Rad customer…

<<<<<<< HEAD

Aug 6, 2009

1L liquid culture (grown for 10 days) was split into two UV-sterilized bottles. Cells were pelleted in a Sorvall T21 centrifuge using the bucket rotor for 30mins @ 4200RPM…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Bacteria - C.pugetti culture (from 20090713)

2009

Miscellaneous

Jul 23, 2009

1L liquid culture (grown for 10 days) was split into two UV-sterilized bottles. Cells were pelleted in a Sorvall T21 centrifuge using the bucket rotor for 30mins @ 4200RPM…

<<<<<<< HEAD

Jul 23, 2009

Due to some weird anomolies seen during my previous qPCRs with the H.crach RNA/cDNA samples (positive controls produced good fluorescence when tested in Column 1 of the…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Gigas DNA for Opticon testing

2009

Miscellaneous

Due to some weird anomolies seen during my previous qPCRs with the H.crach RNA/cDNA samples (positive controls produced good fluorescence when tested in Column 1 of the…

<<<<<<< HEAD

DNased RNA was used for cDNA rxns. [Workup of the amount of RNA used in each rxn (472ng/uL) is here (Google…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RT Rxns - H.crach DNased RNA (from 20090623)

2009

Miscellaneous

DNased RNA was used for cDNA rxns. [Workup of the amount of RNA used in each rxn (472ng/uL) is here (Google…

<<<<<<< HEAD

Samples were first spec’d , since they had not been since their DNase treatement.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

NanoDrop - H.crach DNased RNA (from 20090623)

2009

Miscellaneous

Jul 21, 2009

Samples were first spec’d , since they had not been since their DNase treatement.

<<<<<<< HEAD

Jul 21, 2009

Now that we have a solid positive control, I’ll use the H.crach_h-1fg_intron primers to check the existing cDNA and DNased RNA. qPCR plate layout/set up is here. Anneal temp…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Abalone cDNA (07:12 set from 3/3/2009 by Lisa) and DNased RNA (from 20090623)

2009

Miscellaneous

Jul 20, 2009

Now that we have a solid positive control, I’ll use the H.crach_h-1fg_intron primers to check the existing cDNA and DNased RNA. qPCR plate layout/set up is here. Anneal temp…

<<<<<<< HEAD

Jul 20, 2009

This is to test (again!) the H.crach_h-1fg_intron primers and obtain a working positive control. This gDNA is from Lisa/Nate. Acquired from them 20090717. Don’t know…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Abalone gDNA (H.crach 06:7-1)

2009

Miscellaneous

Jul 17, 2009

This is to test (again!) the H.crach_h-1fg_intron primers and obtain a working positive control. This gDNA is from Lisa/Nate. Acquired from them 20090717. Don’t know…

<<<<<<< HEAD

Jul 17, 2009

This is nearly a repeat of the qPCR earlier today due to the fact that the positive control never amplified. This is being done to check whether or not there is gDNA…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Abalone cDNA (07:12 set from 3/3/2009 by Lisa) and DNased RNA (from 20090623)

2009

Miscellaneous

This is nearly a repeat of the qPCR earlier today due to the fact that the positive control never amplified. This is being done to check whether or not there is gDNA…

<<<<<<< HEAD

This is being done to check whether or not there is gDNA contamination in these cDNA and DNased RNA. Will use H.crach_h-1fg_intron primers. gDNA 07:12-15 was used as a…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Abalone cDNA (07:12 set from 3/3/2009 by Lisa) and DNased RNA (from 20090623)

2009

Miscellaneous

This is being done to check whether or not there is gDNA contamination in these cDNA and DNased RNA. Will use H.crach_h-1fg_intron primers. gDNA 07:12-15 was used as a…

<<<<<<< HEAD

Used up the remainder of the one positive control gDNA that worked with all the primers in yesterday’s reaction (H.crach_h-1fg_intron, H.iris_actin_intron, H.crach_16s), so…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Abalone gDNA

2009

Miscellaneous

Jul 15, 2009

Used up the remainder of the one positive control gDNA that worked with all the primers in yesterday’s reaction (H.crach_h-1fg_intron, H.iris_actin_intron, H.crach_16s), so…

<<<<<<< HEAD

Jul 15, 2009

This was done to really test the detection methods we’re using for gDNA contamination in our qPCRs. qPCR plate layout/set up is here. Anneal temp 50C.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Abalone RNA/DNased RNA & “dirty” and “clean” cDNA

2009

Miscellaneous

Jul 14, 2009

This was done to really test the detection methods we’re using for gDNA contamination in our qPCRs. qPCR plate layout/set up is here. Anneal temp 50C.

<<<<<<< HEAD

Jul 14, 2009

PCR of MIE-14v just to make sure that we can’t get a product from this sample, despite NanoDrop readings suggesting that there’s no DNA. Used both LABY and Euk primer sets. P…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

PCR - Dungan isolate (MIE-14v) gDNA from 20090708

2009

Miscellaneous

PCR of MIE-14v just to make sure that we can’t get a product from this sample, despite NanoDrop readings suggesting that there’s no DNA. Used both LABY and Euk primer sets. P…

<<<<<<< HEAD

One of the three starter liquid cultures from 20090706 wee used to inoculate 1L of Marine Broth + biphenyl. Incubated 200RPM @ 28C.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Bacteria - C.pugetti large culture

2009

Miscellaneous

One of the three starter liquid cultures from 20090706 wee used to inoculate 1L of Marine Broth + biphenyl. Incubated 200RPM @ 28C.

<<<<<<< HEAD

Due to lack of amplification in gDNA samples from 20090710 and 20090708 with either set of intron primers, will repeat with additional gDNA samples to make sure the primers…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Abalone gDNA/cDNA

2009

Miscellaneous

Jul 11, 2009

Due to lack of amplification in gDNA samples from 20090710 and 20090708 with either set of intron primers, will repeat with additional gDNA samples to make sure the primers…

<<<<<<< HEAD

Jul 11, 2009

Ran qPCR on gDNA (06:50-10) to test new primers (H.iris_actin_intron_Fw/Rv) designed to bind only to a region in an intron of the H.iris actin gene. Hopefully there’s enough…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - DNased Abalone Dg RNA from 20090625

2009

Miscellaneous

Jul 10, 2009

Ran qPCR on gDNA (06:50-10) to test new primers (H.iris_actin_intron_Fw/Rv) designed to bind only to a region in an intron of the H.iris actin gene. Hopefully there’s enough…

<<<<<<< HEAD

Jul 10, 2009

Sample was pelleted by spinning in a microcentrifuge @ max speed, 4C for 30mins. Supe was removed and sample CAREFULLY washed with 1mL 70% EtOH. Sample was spun in a…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Precipitation CONTINUED - Dungan MIE-14v gDNA from yesterday

2009

Miscellaneous

Sample was pelleted by spinning in a microcentrifuge @ max speed, 4C for 30mins. Supe was removed and sample CAREFULLY washed with 1mL 70% EtOH. Sample was spun in a…

<<<<<<< HEAD

An additional attempt to get the actin primers to work for use in screening samples for bay/sea scallop hybrids. The scallop_actin_fw primer was used in conjunction with the…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

PCR - Bay/Sea Scallop DNA

2009

Miscellaneous

An additional attempt to get the actin primers to work for use in screening samples for bay/sea scallop hybrids. The scallop_actin_fw primer was used in conjunction with the…

<<<<<<< HEAD

Ran qPCR on DNased Abalone Dg RNA (07:12 Set), gDNA (06:50-10) and clean cDNA (from 20090422) using primers (H.crach_h-1fg_intron_Fw/Rv) designed to bind only to a region in…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - DNased Abalone Dg RNA from 20090625

2009

Miscellaneous

Jul 8, 2009

Ran qPCR on DNased Abalone Dg RNA (07:12 Set), gDNA (06:50-10) and clean cDNA (from 20090422) using primers (H.crach_h-1fg_intron_Fw/Rv) designed to bind only to a region in…

<<<<<<< HEAD

Jul 8, 2009

Added 1/10 volume of 3M NaOAc (pH = 5.2) to sample (10uL) and then 2 volumes of ice cold 100% EtOH to samples (220uL). Mixed thoroughly and incubated O/N @ -20c.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Precipitation - Dungan MIE-14v gDNA from earlier today

2009

Miscellaneous

Added 1/10 volume of 3M NaOAc (pH = 5.2) to sample (10uL) and then 2 volumes of ice cold 100% EtOH to samples (220uL). Mixed thoroughly and incubated O/N @ -20c.

<<<<<<< HEAD

Cells stored in EtOH were pelleted 5000g, 10mins, 25C. A brownish smear was present along the inside of the tube after spinning; not really a pellet per se. Supe was removed…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

gDNA Isolation - Dungan isolate MIE-14v

2009

Miscellaneous

Cells stored in EtOH were pelleted 5000g, 10mins, 25C. A brownish smear was present along the inside of the tube after spinning; not really a pellet per se. Supe was removed…

<<<<<<< HEAD

Set up qPCR with Cv_18s_F/R primers on the following samples that had previously come up negative in both reps using the diluted (1:20) cDNA that Mac had made specifically…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - MV hemocyte cDNA from 20090614

2009

Miscellaneous

Set up qPCR with Cv_18s_F/R primers on the following samples that had previously come up negative in both reps using the diluted (1:20) cDNA that Mac had made specifically…

<<<<<<< HEAD

A recent email from JGI indicates that they are satisfied with the quality of DNA (as seen on 20090601), however their estimate of the gDNA concentration (42ng/uL) means…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Spec Reading - C.pugetti gDNA from 20090526

2009

Miscellaneous

A recent email from JGI indicates that they are satisfied with the quality of DNA (as seen on 20090601), however their estimate of the gDNA concentration (42ng/uL) means…

<<<<<<< HEAD

Set up qPCR with Cv_18s_F/R primers on the following samples that had previously come up negative in both reps using the diluted (1:20) cDNA that Mac had made specifically…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - MV hemocyte cDNA from 20090614

2009

Miscellaneous

Set up qPCR with Cv_18s_F/R primers on the following samples that had previously come up negative in both reps using the diluted (1:20) cDNA that Mac had made specifically…

<<<<<<< HEAD

Inoculated 3 x 5mL Marine Broth + biphenyl crystals (UV sterilized) cultures from frozen stock in 50mL Falcon tubes. Incubated 200RPM, 28C. Will use these are starter…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Bacteria - C. pugetti liquid cultures

2009

Miscellaneous

Inoculated 3 x 5mL Marine Broth + biphenyl crystals (UV sterilized) cultures from frozen stock in 50mL Falcon tubes. Incubated 200RPM, 28C. Will use these are starter…

<<<<<<< HEAD

Set up qPCR with Cv_CIAPIN_F/R primers. This is a second rep. Plate layout/PCR set up is here.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - MV hemocyte cDNA from 20090614

2009

Miscellaneous

Jul 2, 2009

Set up qPCR with Cv_CIAPIN_F/R primers. This is a second rep. Plate layout/PCR set up is here.

<<<<<<< HEAD

Jul 2, 2009

Set up qPCR with Cv_CatY_F/R primers. This is a second rep. Plate layout/PCR set up is here.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - MV hemocyte cDNA from 20090614

2009

Miscellaneous

Set up qPCR with Cv_CatY_F/R primers. This is a second rep. Plate layout/PCR set up is here.

<<<<<<< HEAD

Set up qPCR with Cv_CatL_F/R primers. This is a second rep. Plate layout/PCR set up is here.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - MV hemocyte cDNA from 20090614

2009

Miscellaneous

Set up qPCR with Cv_CatL_F/R primers. This is a second rep. Plate layout/PCR set up is here.

<<<<<<< HEAD

Set up qPCR with Cv_TLR_“short”_F/R primers. This is a second rep. Plate layout/PCR set up is here.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - MV hemocyte cDNA from 20090614

2009

Miscellaneous

Set up qPCR with Cv_TLR_“short”_F/R primers. This is a second rep. Plate layout/PCR set up is here.

<<<<<<< HEAD

Set up qPCR with Cv_BgBL_F/R primers. This is a second rep. Plate layout/PCR set up is here.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCRs - MV hemocyte cDNA from 20090614

2009

Miscellaneous

Jun 30, 2009

Set up qPCR with Cv_BgBL_F/R primers. This is a second rep. Plate layout/PCR set up is here.

<<<<<<< HEAD

Jun 30, 2009

Set up qPCR with Cv_CysB_F/R. Plate layout/PCR set up is here.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCRs - MV hemocyte cDNA from 20090614

2009

Miscellaneous

Jun 29, 2009

Set up qPCR with Cv_CysB_F/R. Plate layout/PCR set up is here.

<<<<<<< HEAD

Jun 29, 2009

Set up qPCR with Cv_18s_F/R primers. Plate layout/PCR set up is here. This is a second rep. Used 1:20 cDNA plate made by Mac as template.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - MV hemocyte cDNA from 20090614

2009

Miscellaneous

Jun 26, 2009

Set up qPCR with Cv_18s_F/R primers. Plate layout/PCR set up is here. This is a second rep. Used 1:20 cDNA plate made by Mac as template.

<<<<<<< HEAD

Jun 26, 2009

Check Abalone RNA for residual gDNA contamination after DNase treatment. Ran qPCR with H.crach_16s_SYB_F/R primers. Plate layout/PCR set up here.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Abalone Dg DNased RNA from yesterday and earlier today

2009

Miscellaneous

Check Abalone RNA for residual gDNA contamination after DNase treatment. Ran qPCR with H.crach_16s_SYB_F/R primers. Plate layout/PCR set up here.

<<<<<<< HEAD

DNase treated Abalone Dg RNA. Followed Ambion’s Turbo DNA-free Kit rigorous protocol. Here are the calcs/workup for the DNase treatment. This used previously untreated RNA.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNase Treatment - Abalone Dg RNA

2009

Miscellaneous

DNase treated Abalone Dg RNA. Followed Ambion’s Turbo DNA-free Kit rigorous protocol. Here are the calcs/workup for the DNase treatment. This used previously untreated RNA.

<<<<<<< HEAD

Set up qPCR with Cv_CIAPIN_F/R primers. Plate layout/PCR set up is here.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCRs - MV hemocyte cDNA from 20090614

2009

Miscellaneous

Set up qPCR with Cv_CIAPIN_F/R primers. Plate layout/PCR set up is here.

<<<<<<< HEAD

DNase treated the 07:12 set of Abalone Dg RNA. Also, respec’d the RNA prior to proceeding. Followed Ambion’s Turbo DNA-free Kit rigorous protocol. Here are the calcs/workup…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNase Treatment - Abalone Dg RNA (07:12 set)

2009

Miscellaneous

DNase treated the 07:12 set of Abalone Dg RNA. Also, respec’d the RNA prior to proceeding. Followed Ambion’s Turbo DNA-free Kit rigorous protocol. Here are the calcs/workup…

<<<<<<< HEAD

Due to the excessive number of times that these samples have been DNased, I’m concerned that the buffer is becoming too concentrated. So, I’m performing an EtOH precip on…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

EtOH Precipitation - DNased Abalone Dg RNA from yesterday AND the 07:12 set (DNased by Lisa 20090306)

2009

Miscellaneous

Jun 23, 2009

Due to the excessive number of times that these samples have been DNased, I’m concerned that the buffer is becoming too concentrated. So, I’m performing an EtOH precip on…

<<<<<<< HEAD

Jun 23, 2009

Set up qPCR with Cv_CatL_F/R primers. Plate layout/PCR set up is here.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - MV hemocyte cDNA from 20090614

2009

Miscellaneous

Set up qPCR with Cv_CatL_F/R primers. Plate layout/PCR set up is here.

<<<<<<< HEAD

Set up qPCR using H.crach_16s_SYBR_F/R primers. Plate layout/set up is here.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - DNased Abalone Dg RNA from earlier today AND the 07:12 set (DNased by Lisa 20090306)

2009

Miscellaneous

Set up qPCR using H.crach_16s_SYBR_F/R primers. Plate layout/set up is here.

<<<<<<< HEAD

This is the 4th time this RNA has been DNased. Performed using Ambion’s Tubro DNA-free Kit. Followed the “rigorous” treatment protocol.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNase Treatment - Abalone Dg DNased RNA 20090610

2009

Miscellaneous

This is the 4th time this RNA has been DNased. Performed using Ambion’s Tubro DNA-free Kit. Followed the “rigorous” treatment protocol.

<<<<<<< HEAD

Set up qPCR with Cv_TLR _short_F/R primers. Plate layout/PCR set up is here.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - MV hemocyte cDNA from 20090614

2009

Miscellaneous

Jun 18, 2009

Set up qPCR with Cv_TLR _short_F/R primers. Plate layout/PCR set up is here.

<<<<<<< HEAD

Jun 18, 2009

Set up qPCR with Cv_BgBL_F/R primers. Plate layout/PCR set up is here.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - MV hemocyte cDNA from 20090614

2009

Miscellaneous

Jun 17, 2009

Set up qPCR with Cv_BgBL_F/R primers. Plate layout/PCR set up is here.

<<<<<<< HEAD

Jun 17, 2009

Due to craziness seen in melting curves, fluorescence, and empty wells from the previous run, will compare SYTO vs. SYBR with select MV cDNAs. Additionally, acquired some…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - MV hemocyte cDNA: Test Immomix (SYTO13) vs. Strategene SYBR

2009

Miscellaneous

Due to craziness seen in melting curves, fluorescence, and empty wells from the previous run, will compare SYTO vs. SYBR with select MV cDNAs. Additionally, acquired some…

<<<<<<< HEAD

qPCR set up/plate layout is here. Used Cv_18s_F/R primers to assess samples’ “useability” for future qPCRs. Used an ABI optically clear adhesive film instead of caps. Ran…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - MV hemocyte cDNA from yesterday

2009

Miscellaneous

qPCR set up/plate layout is here. Used Cv_18s_F/R primers to assess samples’ “useability” for future qPCRs. Used an ABI optically clear adhesive film instead of caps. Ran…

<<<<<<< HEAD

Made cDNA using Promega M-MLV RT and oligo dT primers. RT rxn set up is here. Samples were stored @ 4C until ready to use.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Reverse Transcription - MV hemocyte DNased RNA from 20090612

2009

Miscellaneous

Jun 14, 2009

Made cDNA using Promega M-MLV RT and oligo dT primers. RT rxn set up is here. Samples were stored @ 4C until ready to use.

<<<<<<< HEAD

Jun 14, 2009

qPCR set up/plate layout is here. Used Cv_18s_F/R primers for the MV hemocyte RNA and Gigas_18s_F/R primers for the Turbo kit test. Anneal 55C.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - DNased MV hemocyte RNA from earlier today AND Turbo kit test

2009

Miscellaneous

qPCR set up/plate layout is here. Used Cv_18s_F/R primers for the MV hemocyte RNA and Gigas_18s_F/R primers for the Turbo kit test. Anneal 55C.

<<<<<<< HEAD

Samples 3326: B23, A25, A22, B14, A21, A10 B22 came up positive for gDNA still. These were retreated according to Ambion protocol with a brand new Turbo DNA-free DNase kit.…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNase Treatment - MV hemocyte RNA from yesterday

2009

Miscellaneous

Samples 3326: B23, A25, A22, B14, A21, A10 B22 came up positive for gDNA still. These were retreated according to Ambion protocol with a brand new Turbo DNA-free DNase kit.…

<<<<<<< HEAD

The entire 20uL of RNA were treated with Ambion’s Turbo DNA-free kit according to protocol and spec’d.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNase Treatment - MV hemocyte RNA from earlier today

2009

Miscellaneous

The entire 20uL of RNA were treated with Ambion’s Turbo DNA-free kit according to protocol and spec’d.

<<<<<<< HEAD

Samples were pelleted at 100g, 4C for 10mins. The supe was mostly removed, leaving ~50uL of supe above the pellets. RNA was isolated according to the TriReagent protocol…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation - Martha’s Vineyard (MV) hemocytes

2009

Miscellaneous

Samples were pelleted at 100g, 4C for 10mins. The supe was mostly removed, leaving ~50uL of supe above the pellets. RNA was isolated according to the TriReagent protocol…

<<<<<<< HEAD

This is a repeat of the previous qPCR from earlier today, BUT I think I might have used the wrong primers in the earlier qPCR (see below). Set up qPCR with the correct (I’m…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Re-DNased abalone Dg RNA from earlier today

2009

Miscellaneous

This is a repeat of the previous qPCR from earlier today, BUT I think I might have used the wrong primers in the earlier qPCR (see below). Set up qPCR with the correct (I’m…

<<<<<<< HEAD

Set up qPCR. Plate layout/workup is here.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Re-DNased abalone Dg RNA from earlier today

2009

Miscellaneous

Set up qPCR. Plate layout/workup is here.

<<<<<<< HEAD

This is the 3rd time this will be performed on these samples. Hopefully using a different (i.e. new) kit will work. Not sure what’s going on here. Performed according to…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNase Treatment - Abalone Dg DNased RNA from 20090605

2009

Miscellaneous

This is the 3rd time this will be performed on these samples. Hopefully using a different (i.e. new) kit will work. Not sure what’s going on here. Performed according to…

<<<<<<< HEAD

This is a repeat of yesterday’s PCR due to the presence of bands in the water-only samples. Will use reagents and universal 16s bacterial primers (27F & 1492R) provide by…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

PCR - C.pugetti gDNA from 20090526

2009

Miscellaneous

Jun 9, 2009

This is a repeat of yesterday’s PCR due to the presence of bands in the water-only samples. Will use reagents and universal 16s bacterial primers (27F & 1492R) provide by…

<<<<<<< HEAD

Jun 9, 2009

Previous PCRs from 20090601 & 20090602 both showed contamination in the negative control. Suspect that the primer stocks were contaminated due to the usage of older…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

PCR - C.pugetti gDNA from 20090513 & 20090526

2009

Miscellaneous

Previous PCRs from 20090601 & 20090602 both showed contamination in the negative control. Suspect that the primer stocks were contaminated due to the usage of older…

<<<<<<< HEAD

Done to verify removal of gDNA from RNA. Used H.crach_16s_syb_f/r primers. PCR workup/plate layout is here.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Re-DNased abalone Dg RNA from earlier today

2009

Miscellaneous

Done to verify removal of gDNA from RNA. Used H.crach_16s_syb_f/r primers. PCR workup/plate layout is here.

<<<<<<< HEAD

Had to re-treat these samples due to residual gDNA that was NOT eliminated the first time through. Possible old Ambion kit??

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNase Treatment - Abalone Dg DNased RNA from 20090605

2009

Miscellaneous

Had to re-treat these samples due to residual gDNA that was NOT eliminated the first time through. Possible old Ambion kit??

<<<<<<< HEAD

Inoculated 1x 1L of MB + biphenyl crystals from frozen stock. Incubated 28C, 200RPM. MB was autoclaved with the biphenyl crystals.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Bacteria - C.pugetti culture (1x 1L)

2009

Miscellaneous

Inoculated 1x 1L of MB + biphenyl crystals from frozen stock. Incubated 28C, 200RPM. MB was autoclaved with the biphenyl crystals.

<<<<<<< HEAD

Done to verify removal of gDNA from RNA. Used H.crach_16s_syb_f/r primers. PCR workup/plate layout is here.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - DNased abalone Dg RNA from earlier today

2009

Miscellaneous

Done to verify removal of gDNA from RNA. Used H.crach_16s_syb_f/r primers. PCR workup/plate layout is here.

<<<<<<< HEAD

RNA from yesterday was treated according to Ambion Turbo DNA-free protocol to remove gDNA contamination. Work up is here.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNase Treatment - Abalone Dg RNA isolated yesterday and from 20090518

2009

Miscellaneous

RNA from yesterday was treated according to Ambion Turbo DNA-free protocol to remove gDNA contamination. Work up is here.

<<<<<<< HEAD

RNA was isolated from the following samples using the MoBio RNA PowerSoil Kit according to protocol:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation - Abalone Dg Project Samples

2009

Miscellaneous

Jun 4, 2009

RNA was isolated from the following samples using the MoBio RNA PowerSoil Kit according to protocol:

<<<<<<< HEAD

Jun 4, 2009

RNA from yesterday was treated according to Ambion Turbo DNA-free protocol to remove gDNA contamination. Work up is here. Will check for residual gDNA contamination once…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNase Treatment - Abalone Dg RNA isolated yesterday

2009

Miscellaneous

Jun 3, 2009

RNA from yesterday was treated according to Ambion Turbo DNA-free protocol to remove gDNA contamination. Work up is here. Will check for residual gDNA contamination once…

<<<<<<< HEAD

Jun 3, 2009

This is a repeat of yesterday’s PCR with a fresh working stock in hopes of eliminating the source of contamination seen in the negative control yesterday.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

PCR - C.pugetti DNA from 20090513 & 20090526

2009

Miscellaneous

This is a repeat of yesterday’s PCR with a fresh working stock in hopes of eliminating the source of contamination seen in the negative control yesterday.

<<<<<<< HEAD

Isolated RNA using the MoBio RNA PowerSoil Kit according to protocol from the following samples:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation - Abalone Dg Project

2009

Miscellaneous

Isolated RNA using the MoBio RNA PowerSoil Kit according to protocol from the following samples:

<<<<<<< HEAD

Performed PCR as set up here using universal bacterial 16s primers (sequences provided by Sara Kelly).

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

PCR - C.pugetti DNA from 20090513 & 20090526

2009

Miscellaneous

Performed PCR as set up here using universal bacterial 16s primers (sequences provided by Sara Kelly).

<<<<<<< HEAD

Lane 1 - 15ng standard (5uL)

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Gel - JGI QC check of C. pugetti DNA from 20090526

2009

Miscellaneous

Lane 1 - 15ng standard (5uL)

<<<<<<< HEAD

Followed JGI “Bacterial genomic DNA isolation using CTAB” protocol(Word doc) with the following notes/changes.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

gDNA Isolation - C. pugetti (from 20090518)

2009

Miscellaneous

May 26, 2009

Followed JGI “Bacterial genomic DNA isolation using CTAB” protocol(Word doc) with the following notes/changes.

<<<<<<< HEAD

May 26, 2009

Used BB & DH samples #11-17 for procedure. Followed Epigentek’s protocol. My calcs for dilutions/solutions needed are here. All solutions were made fresh before using…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Methylation Test - Gigas site gDNA (BB & DH) from 20090515

2009

Miscellaneous

May 19, 2009

Used BB & DH samples #11-17 for procedure. Followed Epigentek’s protocol. My calcs for dilutions/solutions needed are here. All solutions were made fresh before using…

<<<<<<< HEAD

May 19, 2009

Isolated RNA from Abalone Dg samples (see below) using MoBio RNA PowerSoil Kit according to protocol. RNA was stored @ -80C.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation - Abalone Dg Project samples

2009

Miscellaneous

Isolated RNA from Abalone Dg samples (see below) using MoBio RNA PowerSoil Kit according to protocol. RNA was stored @ -80C.

<<<<<<< HEAD

Inoculated 2 x 1L of 1x Marine Broth + biphenyl crystals (in 2L flasks) using 5mL of liquid culture from 20090501. Incubated at 28C 200RPM.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

C.pugetti - Liquid Cultures

2009

Miscellaneous

Inoculated 2 x 1L of 1x Marine Broth + biphenyl crystals (in 2L flasks) using 5mL of liquid culture from 20090501. Incubated at 28C 200RPM.

<<<<<<< HEAD

Transferred tissue from previously Chelexed samples:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

gDNA Isolation - Gigas Dermo Samples

2009

Miscellaneous

Transferred tissue from previously Chelexed samples:

<<<<<<< HEAD

Due to failure of gDNA isolation via the TriReagent method (see 20090511) used Qiagen DNeasy Kit. Digested samples for 3 hrs. at 55C in Proteinase K according to protocol.…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

gDNA Isolation - Mac’s BB and DH site samples

2009

PROPS

Due to failure of gDNA isolation via the TriReagent method (see 20090511) used Qiagen DNeasy Kit. Digested samples for 3 hrs. at 55C in Proteinase K according to protocol.…

<<<<<<< HEAD

Performed RT using Promega M-MLV RT according to M-MLV protocol and used 0.5ug oligo dT per ug of RNA on all BB and DH site samples that were negative for gDNA (see qPCR…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Reverse Transcription - Mac’s gigas DNased RNA from 20090512

2009

PROPS

May 14, 2009

Performed RT using Promega M-MLV RT according to M-MLV protocol and used 0.5ug oligo dT per ug of RNA on all BB and DH site samples that were negative for gDNA (see qPCR…

<<<<<<< HEAD

May 14, 2009

Isolated according to JGI protocol (Word doc). Used 100mL, 8 day old culture inoculated from a plate on 20090505. Resuspended pellets in 740uL of TE and took an OD600 via…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

gDNA Isolation - C.pugetti

2009

Miscellaneous

May 13, 2009

Isolated according to JGI protocol (Word doc). Used 100mL, 8 day old culture inoculated from a plate on 20090505. Resuspended pellets in 740uL of TE and took an OD600 via…

<<<<<<< HEAD

May 13, 2009

Performed qPCR on the DNased oyster RNA from earlier today with Gigas_18s_F/R primers to verify removal of detectable gDNA in the samples, since the qPCR from 20090508…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Mac’s gigas DNased RNA from earlier today

2009

PROPS

Performed qPCR on the DNased oyster RNA from earlier today with Gigas_18s_F/R primers to verify removal of detectable gDNA in the samples, since the qPCR from 20090508…

<<<<<<< HEAD

Followed the rigorous protocol for Ambion’s Turbo DNA-free protocol for the following RNAs:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNase Treatment (Rigorous!) - Mac’s gigas RNA/Re-DNased RNA from 20090507 & 20090508, respectively

2009

PROPS

Followed the rigorous protocol for Ambion’s Turbo DNA-free protocol for the following RNAs:

<<<<<<< HEAD

Isolated gDNA according to Molecular Research Center TriReagent protocol from BB#1-20 and DH#1-20. Resuspended DNA in 600uL of 8mM NaOH. Spec.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNA Isolation - Mac’s gigas samples from 20090505 & 20090506

2009

PROPS

May 11, 2009

Isolated gDNA according to Molecular Research Center TriReagent protocol from BB#1-20 and DH#1-20. Resuspended DNA in 600uL of 8mM NaOH. Spec.

<<<<<<< HEAD

May 11, 2009

Performed qPCR on the re-DNased oyster RNA from earlier today with Gigas_18s_F/R primers to verify removal of detectable gDNA in the samples, since the initial qPCR from…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Re-DNased oyster RNA from today

2009

PROPS

Performed qPCR on the re-DNased oyster RNA from earlier today with Gigas_18s_F/R primers to verify removal of detectable gDNA in the samples, since the initial qPCR from…

<<<<<<< HEAD

Yesterday’s qPCR indicated that all of the RNA still contained gDNA contamination. So, took 10ug of RNA from BB #1-10 and DH#1-10 (calcs/workup BB and DH) and brought the…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNase Treatment - Oyster RNA from yesterday

2009

PROPS

Yesterday’s qPCR indicated that all of the RNA still contained gDNA contamination. So, took 10ug of RNA from BB #1-10 and DH#1-10 (calcs/workup BB and DH) and brought the…

<<<<<<< HEAD

Performed qPCR on the DNased RNA to with Gigas_18s_F/R primers to verify removal of detectable gDNA in the samples. Plate layout/set up can be found here.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - DNased oyster RNA from earlier today

2009

PROPS

Performed qPCR on the DNased RNA to with Gigas_18s_F/R primers to verify removal of detectable gDNA in the samples. Plate layout/set up can be found here.

<<<<<<< HEAD

All of the RNA (50uL) was DNase treated with Ambion’s Turbo DNA-free kit according to protocol. Samples were spec’d.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

DNase Treatment - Oyster RNA from today

2009

PROPS

All of the RNA (50uL) was DNase treated with Ambion’s Turbo DNA-free kit according to protocol. Samples were spec’d.

<<<<<<< HEAD

Samples were precipitated according to TriReaget protocol. RNA was resuspended in 50uL of 0.1% DEPC-H2O and then heated @ 55C for 10mins to help dissolve the pellets.…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation - Mac’s oyster tissues (BB and DH) (CONTINUED from yesterday)

2009

PROPS

Samples were precipitated according to TriReaget protocol. RNA was resuspended in 50uL of 0.1% DEPC-H2O and then heated @ 55C for 10mins to help dissolve the pellets.…

<<<<<<< HEAD

Completed the reaminder of the samples (BB#9-20 and DH#1-20) up to the point of precipitation. Isopropanol was added and stored @ -20C. Organic phase was retained for…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation - Mac’s oyster tissues (BB and DH) (CONTINUED from yesterday)

2009

PROPS

May 6, 2009

Completed the reaminder of the samples (BB#9-20 and DH#1-20) up to the point of precipitation. Isopropanol was added and stored @ -20C. Organic phase was retained for…

<<<<<<< HEAD

May 6, 2009

Started two 100mL cultures in 1x Marine Broth + biphenyl. One culture was inoculated from the original liquid culture (from 20090419) and the second was inoculated with a…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Bacteria - C. pugetti liquid cultures

2009

Miscellaneous

Started two 100mL cultures in 1x Marine Broth + biphenyl. One culture was inoculated from the original liquid culture (from 20090419) and the second was inoculated with a…

<<<<<<< HEAD

Processed BB#1-8 up to the point of precipitation. Added isopropanol and stored @ -20C. Organic phase was retained for subsequent gDNA isolation and stored @ 4C.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation - Mac’s oyster tissues (BB and DH)

2009

PROPS

Processed BB#1-8 up to the point of precipitation. Added isopropanol and stored @ -20C. Organic phase was retained for subsequent gDNA isolation and stored @ 4C.

<<<<<<< HEAD

Inoculated a total of 10, 5mL 1x Marine Broth in 50mL conicals. 5 tubes received 1mL of the original culture started on 20090419. 4 tubes received 1mL of the secondary…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Bacteria - C. pugetti liquid cultures

2009

Miscellaneous

May 1, 2009

Inoculated a total of 10, 5mL 1x Marine Broth in 50mL conicals. 5 tubes received 1mL of the original culture started on 20090419. 4 tubes received 1mL of the secondary…

<<<<<<< HEAD

May 1, 2009

An additional yellowing has occurred on the plate. This is in accordance with the Dyksterhouse et al. paper. Colonies still barely visible.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Bacteria - C. pugetti plate (from 20090424)

2009

Miscellaneous

Apr 30, 2009

An additional yellowing has occurred on the plate. This is in accordance with the Dyksterhouse et al. paper. Colonies still barely visible.

<<<<<<< HEAD

Apr 30, 2009

There appears to be growth on the plate. There is a large, bright yellow/chartreuse region on the plate where the streaking was initiated. Additionally, upon close…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Bacteria - C. pugetti plate (from 20090424)

2009

Miscellaneous

Apr 29, 2009

There appears to be growth on the plate. There is a large, bright yellow/chartreuse region on the plate where the streaking was initiated. Additionally, upon close…

<<<<<<< HEAD

Apr 29, 2009

Results: It has now been 8 days since revival of the ATCC freeze dried culture. The media still looks a bit cloudy, but hasn’t really changed since the second or third day…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Bacteria - C. pugetti liquid culture

2009

Miscellaneous

Apr 27, 2009

Results: It has now been 8 days since revival of the ATCC freeze dried culture. The media still looks a bit cloudy, but hasn’t really changed since the second or third day…

<<<<<<< HEAD

Apr 27, 2009

Streaked C. pugetti onto marine broth plate + a few biphenyl crystals and incubated at RT over the weekend.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Bacteria - C. pugetti plate

2009

Miscellaneous

Apr 24, 2009

Streaked C. pugetti onto marine broth plate + a few biphenyl crystals and incubated at RT over the weekend.

<<<<<<< HEAD

Apr 24, 2009

Prepared cDNA using an equal amount of RNA from all samples (442.6ng)(https://spreadsheets.google.com/ccc?key=0AmS_90rPaQMzcHdyU1d0MDVMLWphMFdTOHUwVHFqWnc&hl=en). This…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Reverse Transcription - cDNA from DNased Abalone RNA from 20090420

2009

Miscellaneous

black abalone

DNased RNA

Haliotis cracherodii

M-MLV

reverse transcription

RNA

Apr 22, 2009

Prepared cDNA using an equal amount of RNA from all samples (442.6ng)(https://spreadsheets.google.com/ccc?key=0AmS_90rPaQMzcHdyU1d0MDVMLWphMFdTOHUwVHFqWnc&hl=en). This…

<<<<<<< HEAD

Apr 22, 2009

Performed qPCR to evaluate gDNA removal w/ 2x Immomx and SYTO 13. qPCR/plate set up is here.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Abalone DNased RNA from yesterday

2009

Miscellaneous

Performed qPCR to evaluate gDNA removal w/ 2x Immomx and SYTO 13. qPCR/plate set up is here.

<<<<<<< HEAD

Transferred 1mL of the culture to a 50mL conical containing 4mL of 1x Marine Broth and a couple crystals of biphenyl. Kept the cap loosened and incubated at 20C with shaking…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Bacteria - C. pugettii culture CONTINUED (from 20090419)

2009

Miscellaneous

Transferred 1mL of the culture to a 50mL conical containing 4mL of 1x Marine Broth and a couple crystals of biphenyl. Kept the cap loosened and incubated at 20C with shaking…

<<<<<<< HEAD

Transferred 50uL of RNA to fresh tubes and processed them using the Ambion Turbo DNA-free kit according to the manufacturer’s protocol.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

gDNA Removal - Abalone RNA from 20090402 and 20090331

2009

Miscellaneous

Apr 20, 2009

Transferred 50uL of RNA to fresh tubes and processed them using the Ambion Turbo DNA-free kit according to the manufacturer’s protocol.

<<<<<<< HEAD

Apr 20, 2009

Rehydrated ATCC isolate according to directions. Added 5mL of 1x Marine Broth to a glass culture tube. Used 1mL of this to rehydrate ATCC sample and then added back into the…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Bacteria - C. pugettii culture

2009

Miscellaneous

Apr 19, 2009

Rehydrated ATCC isolate according to directions. Added 5mL of 1x Marine Broth to a glass culture tube. Used 1mL of this to rehydrate ATCC sample and then added back into the…

<<<<<<< HEAD

Apr 19, 2009

Submitted two plates for sequencing. Each sample two times from each direction.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Sequencing - Dungan isolates

2009

Miscellaneous

Apr 17, 2009

Submitted two plates for sequencing. Each sample two times from each direction.

<<<<<<< HEAD

Apr 17, 2009

Repeat of yesterday’s PCR, but with AmpliTaq, less gDNA and 50uL rxn volume. PCR set up is here.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

PCR - Two new Dungan isolates

2009

Miscellaneous

Apr 16, 2009

Repeat of yesterday’s PCR, but with AmpliTaq, less gDNA and 50uL rxn volume. PCR set up is here.

<<<<<<< HEAD

Apr 16, 2009

Attempt to find out if gDNA contamination exists iafter Ambion treatment. Previous test (on 20090414) suggests the QT Kit did not eliminate gDNA. PCR set up and plate layout…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Rab7_SYBR primers on abalone RNA and DNased RNA

2009

Miscellaneous

Attempt to find out if gDNA contamination exists iafter Ambion treatment. Previous test (on 20090414) suggests the QT Kit did not eliminate gDNA. PCR set up and plate layout…

<<<<<<< HEAD

Isolated gDNA from the following two samples:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

PCR - Two new Dungan isolates from earlier today

2009

Miscellaneous

<<<<<<< HEAD

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

gDNA Isolation - Two new Dungan isolates

2009

Miscellaneous

Isolated gDNA from the following two samples:

<<<<<<< HEAD

Anneal 55C. [PCR set up is here (bottom half of sheet)(https://eagle.fish.washington.edu/Arabidopsis/Notebook%20Workup%20Files/20090414-01.jpg).

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

PCR - Test QT Kit with No RT Abalone rxns from 20090408

2009

Miscellaneous

Anneal 55C. [PCR set up is here (bottom half of sheet)(https://eagle.fish.washington.edu/Arabidopsis/Notebook%20Workup%20Files/20090414-01.jpg).

<<<<<<< HEAD

Used higher annealing temps to improve primer specificity, compared to yesterday’s results. PCR set up and plate layout is here.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

PCR - Bay/Sea scallop gDNAs

2009

Miscellaneous

Used higher annealing temps to improve primer specificity, compared to yesterday’s results. PCR set up and plate layout is here.

<<<<<<< HEAD

Used 3 sets of reverse primers:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

PCR - Bay/Sea scallop gDNA isolated earlier today

2009

Miscellaneous

Used 3 sets of reverse primers:

<<<<<<< HEAD

gDNA was isolated using 500uL of 10% Chelex. Samples were heated @ 95C for 1hr w/periodic vortexing. Samples were then spun 16,000g for 5mins @ 4C. Stored @ -20C in Bay x…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

gDNA Isolation - Bay/Sea Scallop and hybrid samples

2009

Miscellaneous

gDNA was isolated using 500uL of 10% Chelex. Samples were heated @ 95C for 1hr w/periodic vortexing. Samples were then spun 16,000g for 5mins @ 4C. Stored @ -20C in Bay x…

<<<<<<< HEAD

Performed a new PCR on the three types of samples listed above with new TOLLIP primers. The new TOLLIP primers (H.discus_806_F/Ab_866_Rv) surround a putative intron. Thus…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

PCR - Abalone gDNA/RNA/cDNA w/new TOLLIP primer

2009

Miscellaneous

Performed a new PCR on the three types of samples listed above with new TOLLIP primers. The new TOLLIP primers (H.discus_806_F/Ab_866_Rv) surround a putative intron. Thus…

<<<<<<< HEAD

Steven had me re-PCR the old Dungan isolates with the new EukA/B primers. Anneal temp 50C. [PCR set up here (bottom half of…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

PCR - Old Dungan isolates #1-35 w/EukA/B primers

2009

Miscellaneous

Steven had me re-PCR the old Dungan isolates with the new EukA/B primers. Anneal temp 50C. [PCR set up here (bottom half of…

<<<<<<< HEAD

Because Rony’s results from her PCR did not match her previous results for the positive controls, I ran the PCRs myself on the controls and the hybrids. Anneal temp 50C. PCR…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

PCR - Bay/Sea scallop hybrids

2009

Miscellaneous

Because Rony’s results from her PCR did not match her previous results for the positive controls, I ran the PCRs myself on the controls and the hybrids. Anneal temp 50C. PCR…

<<<<<<< HEAD

Did PCR with new Euk primers designed by Steven. Should be one step higher taxonomically. PCR set up is here. Aneal temp 50C.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

PCR - Dungan isolates from 20090402 with Euk primers

2009

Miscellaneous

Did PCR with new Euk primers designed by Steven. Should be one step higher taxonomically. PCR set up is here. Aneal temp 50C.

<<<<<<< HEAD

qPCR was performed with 16s_sybr primers on the DNased RNA that Lisa did. Annel temp 55C. Sample set up and plate layout is here.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Check DNased abalone RNA (by Lisa) for gDNA

2009

Miscellaneous

qPCR was performed with 16s_sybr primers on the DNased RNA that Lisa did. Annel temp 55C. Sample set up and plate layout is here.

<<<<<<< HEAD

qPCR was performed with 16s_sybr primers on a subset of the “No RT” cDNA rxns from yesterday at both 55C and 60C. Sample set up and plate layout is here.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Repeat (modified) of yesterday’s abalone cDNA check

2009

Miscellaneous

qPCR was performed with 16s_sybr primers on a subset of the “No RT” cDNA rxns from yesterday at both 55C and 60C. Sample set up and plate layout is here.

<<<<<<< HEAD

qPCR was performed with 16s_sybr primers on a subset of the cDNA rxns and all of the “No RT” rxns from earlier to detect the presence of contaminating gDNA. qPCR was also…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Abalone cDNA (QT) from earlier today

2009

Miscellaneous

qPCR was performed with 16s_sybr primers on a subset of the cDNA rxns and all of the “No RT” rxns from earlier to detect the presence of contaminating gDNA. qPCR was also…

<<<<<<< HEAD

cDNA was made from the above RNA samples using the Qiagen Quantitect RT Kit. The samples were laid out in a PCR plate. 274.2ng of RNA was used in the rxn for each sample…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

cDNA - Abalone RNA from 20090331 & 20090402

2009

Miscellaneous

cDNA was made from the above RNA samples using the Qiagen Quantitect RT Kit. The samples were laid out in a PCR plate. 274.2ng of RNA was used in the rxn for each sample…

<<<<<<< HEAD

Repeat of PCR from 20090403, but using AmpliTaq and 50C annealing temp. PCR set up is here.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

PCR - New Dungan isolates

2009

Miscellaneous

Apr 6, 2009

Repeat of PCR from 20090403, but using AmpliTaq and 50C annealing temp. PCR set up is here.

<<<<<<< HEAD

Apr 6, 2009

Ran PCR with GoTaq on the new Dungan isolate gDNA from yesterday. PCR set up is here. 53C annealing temp.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

PCR - New Dungan isolates

2009

Miscellaneous

Ran PCR with GoTaq on the new Dungan isolate gDNA from yesterday. PCR set up is here. 53C annealing temp.

<<<<<<< HEAD

Abalone RNA isolated from this week was qPCR’s with 16s primers to determine if gDNA contamination was present. PCR/plate layout is here.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Abalone RNA, check for gDNA

2009

Miscellaneous

Abalone RNA isolated from this week was qPCR’s with 16s primers to determine if gDNA contamination was present. PCR/plate layout is here.

<<<<<<< HEAD

gDNA was isolated from the following using the Qiagen DNEasy Kit:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

gDNA Isolation - New Dungan isolates

2009

Miscellaneous

gDNA was isolated from the following using the Qiagen DNEasy Kit:

<<<<<<< HEAD

Total RNA was isolated from the following abalone digestive gland samples using the RNA Powersoil Kit, according to their protocol:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation - Abalone digestive gland samples

2009

Miscellaneous

Total RNA was isolated from the following abalone digestive gland samples using the RNA Powersoil Kit, according to their protocol:

<<<<<<< HEAD

Total RNA was isolated from the following abalone digestive gland samples using the RNA Powersoil Kit, according to their protocol:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation - Abalone digestive gland samples

2009

Miscellaneous

Mar 31, 2009

Total RNA was isolated from the following abalone digestive gland samples using the RNA Powersoil Kit, according to their protocol:

<<<<<<< HEAD

Mar 31, 2009

Total RNA was isolated from the following abalone digestive gland samples using the RNA Powersoil Kit, according to their protocol:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation - Abalone digestive gland samples

2009

Miscellaneous

Mar 27, 2009

Total RNA was isolated from the following abalone digestive gland samples using the RNA Powersoil Kit, according to their protocol:

<<<<<<< HEAD

Mar 27, 2009

Set up qPCR using the following Virginica primers provided by Mac:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Virginica cDNA (see workup sheet below for more info regarding cDNA)

2009

Miscellaneous

Mar 24, 2009

Set up qPCR using the following Virginica primers provided by Mac:

<<<<<<< HEAD

Mar 24, 2009

Submitted four samples (4uL of each) for Agilent Bioanlyzer:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

mRNA Sample Submission Hard clam gill #1 mRNA from 20090313

2009

Miscellaneous

Mar 16, 2009

Submitted four samples (4uL of each) for Agilent Bioanlyzer:

<<<<<<< HEAD

Mar 16, 2009

Precipitation was continued from yesterday. Samples were resuspended in 25uL of The RNA Storage Solution (from PolyAPursit Kit) and spec’d. Samples were stored @ -80C in…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

mRNA Isolation - hard clam gill #1 continued from yesterday

2009

Miscellaneous

Mar 13, 2009

Precipitation was continued from yesterday. Samples were resuspended in 25uL of The RNA Storage Solution (from PolyAPursit Kit) and spec’d. Samples were stored @ -80C in…

<<<<<<< HEAD

Mar 13, 2009

DNased RNA from earlier today was split into four equal parts (175uL = 39.8ug). Three will be used for mRNA isolation and the fourth will remain as total RNA. Three of these…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

mRNA Isolation - hard clam gill #1 DNased RNA from today

2009

Miscellaneous

DNased RNA from earlier today was split into four equal parts (175uL = 39.8ug). Three will be used for mRNA isolation and the fourth will remain as total RNA. Three of these…

<<<<<<< HEAD

DNAsed RNA using Ambion Turbo DNA-free kit, following the rigorous procedure. Diluted total RNA to 0.2ug/uL (Vf = 720uL). Added 1uL DNase and incubated the tube @ 37C for…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Precipitation - Hard clam gill #1 RNA from 20080819

2009

Miscellaneous

DNAsed RNA using Ambion Turbo DNA-free kit, following the rigorous procedure. Diluted total RNA to 0.2ug/uL (Vf = 720uL). Added 1uL DNase and incubated the tube @ 37C for…

<<<<<<< HEAD

This is an exact repeat of the qPCR from earlier today, but using a fresh working stock of the Vtub_16s_V3 primers. The plate layout/qPCR workup is here.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Repeat of qPCR from earlier today with fresh primer working stocks

2009

Miscellaneous

This is an exact repeat of the qPCR from earlier today, but using a fresh working stock of the Vtub_16s_V3 primers. The plate layout/qPCR workup is here.

<<<<<<< HEAD

This is an exact repeat of the qPCR from Friday, but using a fresh aliquot of water for preparation. The plate layout/qPCR workup is here.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Repeat of 20090227 qPCR with clean water

2009

Miscellaneous

This is an exact repeat of the qPCR from Friday, but using a fresh aliquot of water for preparation. The plate layout/qPCR workup is here.

<<<<<<< HEAD

qPCR was performed using SensiMix/SYBR “kit” with DNAsed RNA samples from 20090224. This qPCR used the new V.tub_16s_V3 primers in hopes of getting better amplification;…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - New 16s primers for V.tubiashii Control vs. Autoclaved gigas samples (see 20090224)

2009

Miscellaneous

Feb 27, 2009

qPCR was performed using SensiMix/SYBR “kit” with DNAsed RNA samples from 20090224. This qPCR used the new V.tub_16s_V3 primers in hopes of getting better amplification;…

<<<<<<< HEAD

Feb 27, 2009

This is a repeat of the qPCR from yesterday, but without the 16s and OmpW primer sets due to double peaks in melting curves yesterday. Plate layout/qPCR workup is here.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - Replicate of V.tubiashii Control vs. Autoclaved gigas samples (see yesterday)

2009

Miscellaneous

Feb 25, 2009

This is a repeat of the qPCR from yesterday, but without the 16s and OmpW primer sets due to double peaks in melting curves yesterday. Plate layout/qPCR workup is here.

<<<<<<< HEAD

Feb 25, 2009

qPCR was performed using SensiMix/SYBR “kit” with DNAsed RNA samples and cDNA made earlier today. The plate layout/qPCR workup is here.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

qPCR - V.tubiashii Control vs. Autoclaved gigas samples (see below)

2009

Miscellaneous

qPCR was performed using SensiMix/SYBR “kit” with DNAsed RNA samples and cDNA made earlier today. The plate layout/qPCR workup is here.

<<<<<<< HEAD

Set up the MMLV RT rxns with random primers using ~833ng DNAsed RNA (prepared yesterday) according to the Promega MMLV Product Insert. This procedure is slightly different…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Reverse Transcription - V.tubiashii DNAsed RNA (from yesterday)

2009

Miscellaneous

Set up the MMLV RT rxns with random primers using ~833ng DNAsed RNA (prepared yesterday) according to the Promega MMLV Product Insert. This procedure is slightly different…

<<<<<<< HEAD

RNA was isolated from the Control and V.tub+gigas samples from the 0, 1, & 24hr time points using 1mL TriReagent. No visible pellets. Used 20uL of 0.1%DEPC-H2O to resuspend…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation - V.tubiashii samples from autoclaved gigas exposure (from 20081218)

2009

Miscellaneous

Feb 23, 2009

RNA was isolated from the Control and V.tub+gigas samples from the 0, 1, & 24hr time points using 1mL TriReagent. No visible pellets. Used 20uL of 0.1%DEPC-H2O to resuspend…

<<<<<<< HEAD

Feb 23, 2009

Set up two containers with 3L seawater and 4 gigas in each container. The treated sample contained:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Epigenetics Experiment - Gigas treatment

2009

Miscellaneous

Feb 20, 2009

Set up two containers with 3L seawater and 4 gigas in each container. The treated sample contained:

<<<<<<< HEAD

Feb 20, 2009

Vibrio samples (2-1 and 2-2) from 20090212 were submitted to the mass spec facility.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Sample Submission - V.tubiashii Mass Spec

2009

Miscellaneous

Feb 18, 2009

Vibrio samples (2-1 and 2-2) from 20090212 were submitted to the mass spec facility.

<<<<<<< HEAD

Feb 18, 2009

Sample prep was continued from yesterday. SpeedVac’d final, pooled elutions for 1.5hrs. Stored tubes @ -80C. Will submit samples 2-1 and 2-2 for mass spec analysis.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Trypsin digestion - Vibrio 2D spots CONTINUED (from yesterday)

2009

Miscellaneous

Feb 12, 2009

Sample prep was continued from yesterday. SpeedVac’d final, pooled elutions for 1.5hrs. Stored tubes @ -80C. Will submit samples 2-1 and 2-2 for mass spec analysis.

<<<<<<< HEAD

Feb 12, 2009

Samples were prepared according to Goodlett Lab protocol and incubated O/N on LabQuake.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Trypsin digestion - Vibrio 2D spots from 20081217

2009

Miscellaneous

Feb 11, 2009

Samples were prepared according to Goodlett Lab protocol and incubated O/N on LabQuake.

<<<<<<< HEAD

Feb 11, 2009

Submitted 4uL (108ng/uL) of mRNA from gigas gill (from DATE!; sometime in late August) to the Center for Array Technologies (CART) at UW. Sample was labelled “SR01”.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

mRNA - Submission for Agilent Bioanalyzer

2009

Miscellaneous

Feb 6, 2009

Submitted 4uL (108ng/uL) of mRNA from gigas gill (from DATE!; sometime in late August) to the Center for Array Technologies (CART) at UW. Sample was labelled “SR01”.

<<<<<<< HEAD

Feb 6, 2009

Samples were pelleted and washed with 70% EtOH according to Ambion PolyA Purist protocol. Pellets were resuspended in 10uL of The RNA Storage Solution (included in the…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

mRNA - Precipitation continued from yesterday

2009

Miscellaneous

Jan 23, 2009

Samples were pelleted and washed with 70% EtOH according to Ambion PolyA Purist protocol. Pellets were resuspended in 10uL of The RNA Storage Solution (included in the…

<<<<<<< HEAD

Jan 23, 2009

mRNA was isolated according to Ambion PolyA Purist protocol. After mixing samples with resin, samples were incubated @ RT for 1hr. Samples were washed per the protocol.…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

mRNA Isolation - Hard Clam gill and hemo RNA

2009

Miscellaneous

mRNA was isolated according to Ambion PolyA Purist protocol. After mixing samples with resin, samples were incubated @ RT for 1hr. Samples were washed per the protocol.…

<<<<<<< HEAD

The two RNA samples from yesterday were precipitated and washed according to the Ambion PolyA Purist protocol and resuspended in 50uL of 0.1% DEPC-H2O.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA - Hard clam hemo RNA (from 20090121)

2009

Miscellaneous

Hard clam

hemocyte

Mercenaria mercenaria

mRNA

mRNA enrichment

The two RNA samples from yesterday were precipitated and washed according to the Ambion PolyA Purist protocol and resuspended in 50uL of 0.1% DEPC-H2O.

<<<<<<< HEAD

The 8 hemo samples were pooled and the 4 gonad/d.g. samples were pooled. RNA was isolated. The homo sample was resuspended in 100uL of 0.1%DEPC-H2O and the gonad/d.g. sample…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation - Hard clam hemo (from 20090121)

2009

Miscellaneous

Jan 21, 2009

The 8 hemo samples were pooled and the 4 gonad/d.g. samples were pooled. RNA was isolated. The homo sample was resuspended in 100uL of 0.1%DEPC-H2O and the gonad/d.g. sample…

<<<<<<< HEAD

Jan 21, 2009

Hemos were collected from the remaining 12 clams as before and stored @ -80C. NOTE: 4 hemocyte samples were extremely cloudy. Possibly not hemos? Maybe gonad/d.g.? Gill…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Bleeding/Tissue Collection - Hard Clams

2009

Miscellaneous

Hemos were collected from the remaining 12 clams as before and stored @ -80C. NOTE: 4 hemocyte samples were extremely cloudy. Possibly not hemos? Maybe gonad/d.g.? Gill…

<<<<<<< HEAD

RNA isolated on 20090116 was precipitated over the weekend @ -20C. Samples were treated according to Ambion PolyA Purist protocol and resuspended in 100uL of 0.1% DEPC-H2O.…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA - Precipitation of Hard Clam Hemo RNA from 20090116

2009

Miscellaneous

RNA isolated on 20090116 was precipitated over the weekend @ -20C. Samples were treated according to Ambion PolyA Purist protocol and resuspended in 100uL of 0.1% DEPC-H2O.…

<<<<<<< HEAD

RNA was isolated from hard clam gill (0.08g; from 20090109) and from hard clam hemos (from 20090114). One “unknown” sample (from 20090114) was also processed. Pellets were…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation - Hard clam gill, hemos

2009

Miscellaneous

Jan 16, 2009

RNA was isolated from hard clam gill (0.08g; from 20090109) and from hard clam hemos (from 20090114). One “unknown” sample (from 20090114) was also processed. Pellets were…

<<<<<<< HEAD

Jan 16, 2009

Bled 7 clams from 20090108 and 20090109. Bled clams using a 23g 1.5 needle on a 3mL syringe. Fluid was gathered and ranged from ~0.4-1.0mL. Hemolymph was transferred to…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Bleeding - Hard Clams

2009

Miscellaneous

Bled 7 clams from 20090108 and 20090109. Bled clams using a 23g 1.5 needle on a 3mL syringe. Fluid was gathered and ranged from ~0.4-1.0mL. Hemolymph was transferred to…

<<<<<<< HEAD

Transferred supe to a fresh tube and added 1mL 70% EtOH to remaining pellet. Spun samples max speed @ 4C 30 mins. Removed supe and washed pellets with 1mL 70% EtOH. Spun max…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA - Precipitation continued from yesterday

2009

Miscellaneous

Transferred supe to a fresh tube and added 1mL 70% EtOH to remaining pellet. Spun samples max speed @ 4C 30 mins. Removed supe and washed pellets with 1mL 70% EtOH. Spun max…

<<<<<<< HEAD

Because of the relatively large size of the pellets vs. the amount of RNA, I think another round of precipitation would be best to help remove additional residual salt…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA - Reprecipitation of hard clam RNA from yesterday

2009

Miscellaneous

Jan 13, 2009

Because of the relatively large size of the pellets vs. the amount of RNA, I think another round of precipitation would be best to help remove additional residual salt…

<<<<<<< HEAD

Jan 13, 2009

Bled 8 clams from 20090108 and 20090109, #4, 6, 8, 15, 16, 17, 21, 26. Bled clams using a 23g 1.5 needle on a 3mL syringe. Fluid was gathered and ranged from ~0.4-1.0mL.…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Bleeding - Hard Clams

2009

Miscellaneous

Bled 8 clams from 20090108 and 20090109, #4, 6, 8, 15, 16, 17, 21, 26. Bled clams using a 23g 1.5 needle on a 3mL syringe. Fluid was gathered and ranged from ~0.4-1.0mL.…

<<<<<<< HEAD

1mL of TriReagent was used to isolate RNA from 3 combined tubes of hemolymph. This resulted in 10 total RNA preps. Pellets were resuspended in 100uL of 0.1% DEPC-H2O and…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation - Hard Clam hemolymph from 20090108, 20090109

2009

Miscellaneous

1mL of TriReagent was used to isolate RNA from 3 combined tubes of hemolymph. This resulted in 10 total RNA preps. Pellets were resuspended in 100uL of 0.1% DEPC-H2O and…

<<<<<<< HEAD

Bled 24 hard clams using a 23g 1.5 needle on a 3mL syringe. Fluid was gathered and ranged from ~0.4-1.0mL. Hemolymph was transferred to individual 1.5mL snap cap tubes and…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Bleeding - Hard Clams

2009

Miscellaneous

Jan 9, 2009

Bled 24 hard clams using a 23g 1.5 needle on a 3mL syringe. Fluid was gathered and ranged from ~0.4-1.0mL. Hemolymph was transferred to individual 1.5mL snap cap tubes and…

<<<<<<< HEAD

Jan 9, 2009

Bled 6 hard clams using a 23g 1.5 needle on a 3mL syringe. Fluid was gathered and ranged from ~0.4-1.0mL. Hemolymph was transferred to individual 1.5mL snap cap tubes and…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Bleeding - Hard Clams

2009

Miscellaneous

Jan 8, 2009

Bled 6 hard clams using a 23g 1.5 needle on a 3mL syringe. Fluid was gathered and ranged from ~0.4-1.0mL. Hemolymph was transferred to individual 1.5mL snap cap tubes and…

<<<<<<< HEAD

Jan 8, 2009

Samples (in Chelex) were vortexed and heated @ 95C for 30mins with periodic vortexing. Tubes were spun max speed @ 4C for 2 mins to pellet Chelex. Set up PCR using Immomix…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

PCR - Dungan Isolates

2009

Miscellaneous

Jan 7, 2009

Samples (in Chelex) were vortexed and heated @ 95C for 30mins with periodic vortexing. Tubes were spun max speed @ 4C for 2 mins to pellet Chelex. Set up PCR using Immomix…

<<<<<<< HEAD

Jan 7, 2009

All samples , except xCVC-11t, are already in Chelex. For xCvC-11t, pipetted a shunk of cells/tissue from source tube. Volume of liquid (EtOH) was ~75uL. Added this to screw…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

PCR - Dungan Isolates

2009

Miscellaneous

Jan 6, 2009

All samples , except xCVC-11t, are already in Chelex. For xCvC-11t, pipetted a shunk of cells/tissue from source tube. Volume of liquid (EtOH) was ~75uL. Added this to screw…

<<<<<<< HEAD

Jan 6, 2009

Pacific oysters, a mussel, barnacles and a clam (sp. ?) were transferred from the holding tank to a large beaker with sea water which was placed into a 37C water bath. The…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

SDS/PAGE, Western Blot - Test of HSP70 Ab on heat stressed shellfish for FISH441

2009

Miscellaneous

Jan 2, 2009

Pacific oysters, a mussel, barnacles and a clam (sp. ?) were transferred from the holding tank to a large beaker with sea water which was placed into a 37C water bath. The…

<<<<<<< HEAD

Jan 2, 2009

Ran varying amounts of Gigas Gill 24hr Control protein extract from 20080917 (Notebook link dead - in genefish.wikispaces notebook). See table below:

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

SDS/PAGE, Western Blot - Test of new Western Breeze Kit & HSP70 Ab for FISH441

2008

Miscellaneous

anti-HSP70

anti-myc

antibody

Coomassie

Crassostrea gigas

MSTN

MSTN1b

myostatin

Pacific oyster

protein

SDS-PAGE

SeeBlue Plus

Western blot

Western Breeze Chromogenic (anti-mouse) Kit

Dec 31, 2008

Ran varying amounts of Gigas Gill 24hr Control protein extract from 20080917 (Notebook link dead - in genefish.wikispaces notebook). See table below:

<<<<<<< HEAD

Dec 31, 2008

Lane 1 - Empty Lane 2 - Total RNA, Control Lane 3 - mRNA, Control Lane 4 - Total RNA, Vibrio+gigas Lane 5 - mRNA, Vibrio+gigas

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Gel - V. tubiashii mRNA samples (from 20081224)

2008

Miscellaneous

Dec 29, 2008

Lane 1 - Empty Lane 2 - Total RNA, Control Lane 3 - mRNA, Control Lane 4 - Total RNA, Vibrio+gigas Lane 5 - mRNA, Vibrio+gigas

<<<<<<< HEAD

Dec 29, 2008

rRNA removal was continued from O/N precipitation. Processed the samples according to the Ambion MICROBExpress Kit protocol and resuspended final pellets in 25uL of The RNA…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

rRNA Removal - V. tubiashii total RNA from yesterday

2008

Miscellaneous

Dec 24, 2008

rRNA removal was continued from O/N precipitation. Processed the samples according to the Ambion MICROBExpress Kit protocol and resuspended final pellets in 25uL of The RNA…

<<<<<<< HEAD

Dec 24, 2008

Added 10mL TriReagent to 2 x 50mL pellets (5.63 x 10^11 total bacteria; see calcs on 20081219 from the control samples collected on 20081219. Added 10mL TriReagent to 1 x…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

RNA Isolation - V. tubiashii from challenge (see 20081216)

2008

Miscellaneous

MICROBExpress Kit

NanoDrop1000

RNA isolation

RNA quantification

TriReagent

Vibrio tubiashii

Dec 22, 2008

Added 10mL TriReagent to 2 x 50mL pellets (5.63 x 10^11 total bacteria; see calcs on 20081219 from the control samples collected on 20081219. Added 10mL TriReagent to 1 x…

<<<<<<< HEAD

Dec 22, 2008

Significantly more bacteria in the container containing autoclaved oysters. Collected 2 x 50mL from each treatment. Collected ~750mL from each treatment. Cells were pelleted…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Vibrio challenge CONTINUED (from yesterday)

2008

Miscellaneous

Dec 19, 2008

Significantly more bacteria in the container containing autoclaved oysters. Collected 2 x 50mL from each treatment. Collected ~750mL from each treatment. Cells were pelleted…

<<<<<<< HEAD

Dec 19, 2008

500mL culture was split evenly between two containers containing 3L sterile sea water each. One container also contained 3 large, autoclaved C. gigas. Containers had an air…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Vibrio challenge CONTINUED (from yesterday)

2008

Miscellaneous

Dec 18, 2008

500mL culture was split evenly between two containers containing 3L sterile sea water each. One container also contained 3 large, autoclaved C. gigas. Containers had an air…

<<<<<<< HEAD

Dec 18, 2008

One of the two starter cultures from yesterday were used to inoculate 500mL 1x LB+1% NaCl and incubated O/N @ 30C 200RPM.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Vibrio challenge CONTINUED (from yesterday)

2008

Miscellaneous

Dec 17, 2008

One of the two starter cultures from yesterday were used to inoculate 500mL 1x LB+1% NaCl and incubated O/N @ 30C 200RPM.

<<<<<<< HEAD

Dec 17, 2008

2X 10mL starter cultures of in 1x LB+1% NaCl were inoculated with two separate colonies of V. tubiashii and incubated O/N @ 30C 200RPM.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Vibrio challenge

2008

Miscellaneous

bacterial challenge

bacterial culture

Vibrio exposure

Vibrio tubiashii

2X 10mL starter cultures of in 1x LB+1% NaCl were inoculated with two separate colonies of V. tubiashii and incubated O/N @ 30C 200RPM.

<<<<<<< HEAD

Another attempt to determine appropriate amounts of anti-HSP70 Ab (ABR cat# MA3-006)and/or protein needed for better detection of HSP70 in Gigas protein samples. Gigas gill…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

SDS/PAGE/Western - anti-HSP70 Ab Re-test

2008

Miscellaneous

anti-HSP70

antibody

chemiluminescent

Coomassie

Crassostrea gigas

hemocyte

hemolymph

Pacific oyster

protein

SDS-PAGE

SeeBlue Plus

Another attempt to determine appropriate amounts of anti-HSP70 Ab (ABR cat# MA3-006)and/or protein needed for better detection of HSP70 in Gigas protein samples. Gigas gill…

<<<<<<< HEAD

Will use two different antibodies and two different development methods: chromogenic (Invitrogen Western Breeze) and chemiluminescent.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

SDS/PAGE/Western - Attempt to fix/identify problem(s) with Westerns

2008

Miscellaneous

Dec 12, 2008

Will use two different antibodies and two different development methods: chromogenic (Invitrogen Western Breeze) and chemiluminescent.

<<<<<<< HEAD

Dec 12, 2008

Primary Ab (anti-HSP70) solution was saved and stored in the 4C. The membrane was washed 3x 10 mins. w/1x TBS-T. 15mL blocking solution was added to membrane and incubated…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

SDS/PAGE/Western - anti-HSP70 Ab test CONTINUED (from yesterday)

2008

Miscellaneous

Dec 10, 2008

Primary Ab (anti-HSP70) solution was saved and stored in the 4C. The membrane was washed 3x 10 mins. w/1x TBS-T. 15mL blocking solution was added to membrane and incubated…

<<<<<<< HEAD

Dec 10, 2008

Test of the new anti-HSP70 Ab (ABR cat# MA3-006). Gigas gill protein extracts from 20080617 (both control and Vibrio exposure samples) were each pooled to result in 10ug…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

SDS/PAGE/Western - anti-HSP70 Ab test

2008

Miscellaneous

anti-HSP70

antibody

Coomassie

Crassostrea gigas

gill

mucus

Octopus rubescans

Pacific oyster

protein

red octopus

SDS-PAGE

skin

Dec 9, 2008

Test of the new anti-HSP70 Ab (ABR cat# MA3-006). Gigas gill protein extracts from 20080617 (both control and Vibrio exposure samples) were each pooled to result in 10ug…

<<<<<<< HEAD

Dec 9, 2008

10uL of each sample from 20081112 (binding supe, washes and elution fractions) were mixed with 2x sample reducing buffer and boiled 5 mins. Samples were loaded onto Pierce…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

SDS/PAGE/Western - Purified (His column) FST samples from 20081112

2008

Miscellaneous

Nov 17, 2008

10uL of each sample from 20081112 (binding supe, washes and elution fractions) were mixed with 2x sample reducing buffer and boiled 5 mins. Samples were loaded onto Pierce…

<<<<<<< HEAD

Nov 17, 2008

Purified bands were delivered for sequencing. See sequencing log for plate layout/primers.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Sequencing - Y2H colony PCRs from 20081112

2008

Myostatin Interacting Proteins

Purified bands were delivered for sequencing. See sequencing log for plate layout/primers.

<<<<<<< HEAD

Trypsin digested band from MSTN1b + red muscle extract co-IP (~75kDa) was delivered for mass spec analysis. Data in 2-3 weeks.

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Mass Spec - Band #1 from 20081106

2008

Myostatin Interacting Proteins

Trypsin digested band from MSTN1b + red muscle extract co-IP (~75kDa) was delivered for mass spec analysis. Data in 2-3 weeks.

<<<<<<< HEAD

10uL of each sample from yesterday (binding supe, washes and elution fractions) were mixed with 2x sample reducing buffer and boiled 5 mins. Samples were loaded onto Pierce…

=======

>>>>>>> 12933cda86d8249f42024c4dce5d6e1c6b871c07

Western Blot - Purified (His column) decorin, FST, LAP & telethonin

2008

Myostatin Interacting Proteins

Nov 13, 2008